Variant report

Variant	rs41398350
Chromosome Location	chr4:76599439-76599440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:76597601-76599571	K562	blood:	n/a	n/a
2	POLR2A	chr4:76597188-76599596	PBDE	blood:	n/a	n/a
3	STAT3	chr4:76599184-76599510	MCF10A-Er-Src	breast:	n/a	chr4:76599426-76599434
4	TBL1XR1	chr4:76598398-76599758	K562	blood:	n/a	n/a
5	IRF1	chr4:76597750-76599470	K562	blood:	n/a	chr4:76597806-76597826 chr4:76598592-76598606 chr4:76598673-76598682 chr4:76597958-76597978 chr4:76598781-76598794
6	HEY1	chr4:76597956-76599534	K562	blood:	n/a	chr4:76598825-76598834
7	CHD2	chr4:76597033-76599783	K562	blood:	n/a	chr4:76597896-76597906
8	POLR2A	chr4:76597599-76599556	K562	blood:	n/a	n/a
9	POLR2A	chr4:76597083-76599672	HepG2	liver:	n/a	n/a
10	POLR2A	chr4:76597623-76599707	GM18505	blood:	n/a	n/a
11	MAFK	chr4:76598611-76599622	K562	blood:	n/a	n/a
12	POLR2A	chr4:76597436-76599499	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr4:76597583-76599511	GM15510	blood:	n/a	n/a
14	POLR2A	chr4:76597467-76599598	GM12891	blood:	n/a	n/a
15	POLR2A	chr4:76597441-76599611	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAZ	chr4:76596859-76599764	IMR90	lung:	n/a	n/a
17	ZC3H11A	chr4:76598756-76599479	K562	blood:	n/a	n/a
18	POLR2A	chr4:76597596-76599449	HUVEC	blood vessel:	n/a	n/a
19	ATF1	chr4:76598515-76599544	K562	blood:	n/a	n/a
20	BHLHE40	chr4:76598350-76599448	K562	blood:	n/a	n/a
21	POLR2A	chr4:76595228-76599606	K562	blood:	n/a	n/a
22	POLR2A	chr4:76597734-76599648	K562	blood:	n/a	n/a
23	POLR2A	chr4:76597596-76599476	GM19193	blood:	n/a	n/a
24	POLR2A	chr4:76596851-76599677	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:76597623-76599538	K562	blood:	n/a	n/a
26	MYC	chr4:76597593-76599458	K562	blood:	n/a	n/a
27	POLR2A	chr4:76597617-76599609	Raji	blood:	n/a	n/a
28	POLR2A	chr4:76596881-76599467	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:76596390-76599553	GM12878	blood:	n/a	n/a
30	HCFC1	chr4:76597622-76599473	K562	blood:	n/a	n/a
31	POLR2A	chr4:76597462-76599518	GM12892	blood:	n/a	n/a
32	RELA	chr4:76597726-76599498	GM10847	blood:	n/a	n/a
33	CHD1	chr4:76597297-76599514	H1-hESC	embryonic stem cell:	n/a	chr4:76597896-76597906
34	POLR2A	chr4:76596931-76599607	GM12878	blood:	n/a	n/a
35	MXI1	chr4:76596757-76599840	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr4:76598209-76599507	U87	brain:	n/a	n/a
37	POLR2A	chr4:76599205-76599581	GM12891	blood:	n/a	n/a
38	POLR2A	chr4:76597704-76599604	HepG2	liver:	n/a	n/a
39	POLR2A	chr4:76597583-76599474	K562	blood:	n/a	n/a
40	POLR2A	chr4:76597039-76599767	GM12891	blood:	n/a	n/a
41	POLR2A	chr4:76596983-76599722	GM12892	blood:	n/a	n/a
42	MXI1	chr4:76597326-76599467	GM12878	blood:	n/a	n/a
43	GTF2F1	chr4:76598382-76599477	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr4:76597626-76599760	MCF10A-Er-Src	breast:	n/a	n/a
45	JUND	chr4:76597688-76599660	K562	blood:	n/a	n/a
46	POLR2A	chr4:76597641-76599580	GM12892	blood:	n/a	n/a
47	POLR2A	chr4:76597556-76599667	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:76597384-76599590	HL-60	blood:	n/a	n/a
49	POLR2A	chr4:76597686-76599635	K562	blood:	n/a	n/a
50	MAZ	chr4:76597644-76599495	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:76436258..76441363-chr4:76597157..76599917,7	K562	blood:
2	chr4:76595601..76600505-chr4:76645864..76652704,29	K562	blood:
3	chr4:76580944..76583542-chr4:76596776..76599526,2	MCF-7	breast:
4	chr4:76596470..76600480-chr4:76647707..76650691,10	MCF-7	breast:
5	chr4:76596286..76601002-chr4:76645864..76652581,23	K562	blood:
6	chr4:76437052..76441363-chr4:76597688..76599751,3	K562	blood:
7	chr4:76595422..76600363-chr4:76647674..76651574,9	MCF-7	breast:
8	chr4:76597989..76600371-chr4:100870169..100871877,2	K562	blood:

No data

Variant related genes	Relation type
G3BP2	TF binding region
ENSG00000164032	Chromatin interaction
ENSG00000138757	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000138768	Chromatin interaction
ENSG00000163743	Chromatin interaction
ENSG00000174796	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs17000766	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801838	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2017607	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2037012	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs324694	1.00[CHD][hapmap]
rs324706	1.00[CHD][hapmap]
rs324734	1.00[CHD][hapmap]
rs56084244	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56151783	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56308338	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56693719	0.94[AMR][1000 genomes]
rs56728961	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57008925	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57099382	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58140957	0.94[AMR][1000 genomes]
rs58822138	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59405026	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59448225	1.00[AMR][1000 genomes]
rs60332325	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66606482	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67662392	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6812339	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs68155345	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6817228	1.00[ASN][1000 genomes]
rs6818849	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821144	0.94[AMR][1000 genomes]
rs6823013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6828587	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6841290	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841486	1.00[ASN][1000 genomes]
rs6843244	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857983	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72649405	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72649420	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
3	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41398350	CSTB	trans	lymphoblastoid	seeQTL
rs41398350	FAM47E	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76596400-76599600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr4:76596600-76599800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr4:76597200-76599600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr4:76598400-76599600	Active TSS	Brain Germinal Matrix	brain
5	chr4:76598800-76599600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr4:76598800-76599600	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr4:76598800-76599600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr4:76598800-76599600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr4:76598800-76599600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:76598800-76599600	Flanking Active TSS	Fetal Brain Male	brain
11	chr4:76598800-76599600	Flanking Active TSS	Fetal Heart	heart
12	chr4:76598800-76599600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr4:76598800-76599600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr4:76598800-76599600	Flanking Active TSS	HMEC	breast
15	chr4:76598800-76599600	Flanking Active TSS	HUVEC	blood vessel
16	chr4:76599000-76599600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:76599000-76599600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr4:76599000-76599600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:76599000-76599600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr4:76599000-76599600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr4:76599000-76599600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:76599000-76599600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr4:76599000-76599600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:76599000-76599600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr4:76599000-76599600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr4:76599000-76599600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:76599000-76599600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:76599000-76599600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:76599000-76599600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:76599000-76599600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr4:76599000-76599600	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr4:76599000-76599600	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr4:76599000-76599600	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr4:76599000-76599600	Flanking Active TSS	Fetal Kidney	kidney
35	chr4:76599000-76599600	Flanking Active TSS	Fetal Lung	lung
36	chr4:76599000-76599600	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr4:76599000-76599600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr4:76599000-76599600	Flanking Active TSS	Stomach Mucosa	stomach
39	chr4:76599000-76599600	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr4:76599000-76599600	Enhancers	Spleen	Spleen
41	chr4:76599000-76599600	Flanking Active TSS	A549	lung
42	chr4:76599000-76599600	Flanking Active TSS	Hela-S3	cervix
43	chr4:76599000-76599600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr4:76599000-76599600	Flanking Active TSS	NHLF	lung
45	chr4:76599000-76599600	Flanking Active TSS	Osteobl	bone
46	chr4:76599000-76599800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:76599000-76599800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:76599000-76599800	Flanking Active TSS	Dnd41	blood
49	chr4:76599000-76599800	Flanking Active TSS	GM12878-XiMat	blood
50	chr4:76599000-76599800	Flanking Active TSS	NHEK	skin

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