Variant report

Variant	rs4950390
Chromosome Location	chr1:146717370-146717371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr1:146716972-146717413	GM12878	blood:	n/a	n/a
2	RCOR1	chr1:146716745-146718056	K562	blood:	n/a	n/a
3	FOS	chr1:146717294-146717701	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:146717355-146717614	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr1:146716784-146717851	K562	blood:	n/a	n/a
6	FOS	chr1:146717296-146717699	MCF10A-Er-Src	breast:	n/a	n/a
7	CBX3	chr1:146717179-146717716	K562	blood:	n/a	n/a
8	JUND	chr1:146717356-146717613	HepG2	liver:	n/a	chr1:146717475-146717486
9	SETDB1	chr1:146717319-146717967	U2OS	brain:	n/a	n/a
10	MAX	chr1:146717363-146717610	K562	blood:	n/a	n/a
11	MYC	chr1:146717348-146717702	MCF10A-Er-Src	breast:	n/a	n/a
12	ARID3A	chr1:146716678-146718269	K562	blood:	n/a	n/a
13	MAFF	chr1:146716785-146717889	K562	blood:	n/a	n/a
14	ZNF384	chr1:146716798-146717686	K562	blood:	n/a	n/a
15	MAX	chr1:146717347-146717704	K562	blood:	n/a	n/a
16	FOXA1	chr1:146717363-146717785	HepG2	liver:	n/a	n/a
17	JUND	chr1:146716703-146717742	K562	blood:	n/a	chr1:146717475-146717486
18	TEAD4	chr1:146716701-146717754	K562	blood:	n/a	n/a
19	MAFK	chr1:146716512-146717737	K562	blood:	n/a	n/a
20	GATA1	chr1:146716314-146717902	PBDE	blood:	n/a	n/a
21	FOS	chr1:146717301-146717709	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr1:146717292-146717627	MCF10A-Er-Src	breast:	n/a	n/a
23	TBL1XR1	chr1:146716458-146717607	K562	blood:	n/a	n/a
24	BHLHE40	chr1:146716609-146717610	K562	blood:	n/a	n/a
25	MAZ	chr1:146716830-146717673	K562	blood:	n/a	n/a
26	EP300	chr1:146716644-146717733	K562	blood:	n/a	n/a
27	ATF3	chr1:146717283-146717622	K562	blood:	n/a	n/a
28	JUN	chr1:146717236-146717651	K562	blood:	n/a	n/a
29	SIRT6	chr1:146716616-146717413	K562	blood:	n/a	n/a
30	MYC	chr1:146716683-146717749	K562	blood:	n/a	n/a
31	UBTF	chr1:146716791-146717756	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:146637222..146651713-chr1:146712141..146718911,44	MCF-7	breast:
2	chr1:146550590..146559110-chr1:146711930..146718078,31	K562	blood:
3	chr1:146714725..146717432-chr1:146860214..146861781,2	MCF-7	breast:
4	chr1:146638562..146647588-chr1:146711453..146720391,22	K562	blood:
5	chr1:146552515..146557737-chr1:146711619..146718083,31	K562	blood:
6	chr1:146640645..146647502-chr1:146711418..146719354,29	K562	blood:
7	chr1:146716123..146718534-chr1:146720847..146724367,3	MCF-7	breast:

No data

Variant related genes	Relation type
FMO5	TF binding region
ENSG00000201142	Chromatin interaction
ENSG00000230832	Chromatin interaction
ENSG00000180867	Chromatin interaction
ENSG00000273071	Chromatin interaction
ENSG00000271721	Chromatin interaction
ENSG00000237188	Chromatin interaction
ENSG00000131791	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10793652	0.81[AMR][1000 genomes]
rs11239953	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11239955	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11239956	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12092016	0.82[AMR][1000 genomes]
rs12093458	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12736102	0.82[ASN][1000 genomes]
rs1890041	0.82[AMR][1000 genomes]
rs1932978	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4950391	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6593750	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6593752	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6704497	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7519804	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7548820	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
7	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv872257	chr1:146643555-146724923	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
22	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
25	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
26	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
27	nsv872259	chr1:146688941-146724923	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4950390	CHD1L	Cis_1M	lymphoblastoid	RTeQTL
rs4950390	CHD1L	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146714200-146717400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:146715400-146722000	Weak transcription	Lung	lung
3	chr1:146715400-146724200	Weak transcription	Esophagus	oesophagus
4	chr1:146715600-146717400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:146715600-146727400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:146715600-146736200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:146715600-146749400	Weak transcription	Colonic Mucosa	Colon
8	chr1:146715800-146717800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr1:146715800-146718800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:146715800-146718800	Weak transcription	Stomach Mucosa	stomach
11	chr1:146715800-146718800	Weak transcription	Thymus	Thymus
12	chr1:146715800-146719000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:146715800-146731400	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:146715800-146756800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:146716000-146717400	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:146716000-146717400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:146716000-146717800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:146716000-146718200	Weak transcription	Fetal Lung	lung
19	chr1:146716000-146718600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:146716000-146718800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:146716000-146718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:146716000-146718800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:146716000-146718800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:146716000-146718800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:146716000-146718800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:146716000-146718800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:146716000-146718800	Weak transcription	Right Ventricle	heart
28	chr1:146716000-146718800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:146716000-146718800	Weak transcription	Small Intestine	intestine
30	chr1:146716000-146718800	Weak transcription	HSMM	muscle
31	chr1:146716000-146719000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:146716000-146719000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:146716000-146719000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:146716000-146719000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:146716000-146719000	Weak transcription	Brain Angular Gyrus	brain
36	chr1:146716000-146719000	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:146716000-146719000	Weak transcription	Right Atrium	heart
38	chr1:146716000-146719000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:146716000-146719200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:146716000-146719600	Enhancers	Liver	Liver
41	chr1:146716000-146719800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:146716000-146720200	Weak transcription	HUVEC	blood vessel
43	chr1:146716000-146722000	Weak transcription	Fetal Intestine Small	intestine
44	chr1:146716000-146724200	Weak transcription	Fetal Stomach	stomach
45	chr1:146716000-146726000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:146716000-146727200	Weak transcription	Fetal Intestine Large	intestine
47	chr1:146716000-146727200	Weak transcription	NH-A	brain
48	chr1:146716000-146727400	Weak transcription	Adipose Nuclei	Adipose
49	chr1:146716000-146727400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:146716000-146727400	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links