Variant report

Variant	rs10798295
Chromosome Location	chr1:173683954-173683955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:522)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:522 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:173683692-173684733	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr1:173683839-173684499	H1-hESC	embryonic stem cell:	n/a	chr1:173684241-173684251
3	SIX5	chr1:173683779-173684123	GM12878	blood:	n/a	n/a
4	MAZ	chr1:173683774-173684585	GM12878	blood:	n/a	n/a
5	TEAD4	chr1:173683773-173684382	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr1:173683795-173684744	GM15510	blood:	n/a	n/a
7	REST	chr1:173683849-173684612	ECC-1	luminal epithelium:	n/a	chr1:173684253-173684262
8	SETDB1	chr1:173683654-173684241	U2OS	brain:	n/a	n/a
9	MYC	chr1:173683843-173684237	MCF10A-Er-Src	breast:	n/a	n/a
10	BATF	chr1:173683895-173684171	GM12878	blood:	n/a	n/a
11	JUND	chr1:173683854-173684382	A549	lung:	n/a	n/a
12	POLR2A	chr1:173683793-173684446	GM12891	blood:	n/a	n/a
13	POLR2A	chr1:173683671-173684437	HCT-116	colon:	n/a	n/a
14	RCOR1	chr1:173683847-173684804	K562	blood:	n/a	n/a
15	SIN3AK20	chr1:173683798-173684808	SK-N-SH	brain:	n/a	n/a
16	JUND	chr1:173683785-173684720	K562	blood:	n/a	n/a
17	CEBPB	chr1:173683699-173684683	Hela-S3	cervix:	n/a	n/a
18	BRCA1	chr1:173683877-173684260	HepG2	liver:	n/a	n/a
19	TAF1	chr1:173683763-173684358	GM12892	blood:	n/a	n/a
20	SRF	chr1:173683886-173684203	H1-hESC	embryonic stem cell:	n/a	n/a
21	EP300	chr1:173683849-173684263	HepG2	liver:	n/a	chr1:173683991-173683998 chr1:173684063-173684072
22	MAX	chr1:173683719-173684577	MCF-7	breast:	n/a	n/a
23	TAF1	chr1:173683844-173684355	GM12891	blood:	n/a	n/a
24	MAFK	chr1:173683773-173684620	Hela-S3	cervix:	n/a	n/a
25	GABPA	chr1:173683730-173684464	HL-60	blood:	n/a	n/a
26	POLR2A	chr1:173683763-173684429	SK-N-MC	brain:	n/a	n/a
27	HDAC2	chr1:173683887-173684466	K562	blood:	n/a	n/a
28	SMARCC1	chr1:173683536-173684829	Hela-S3	cervix:	n/a	n/a
29	TAF1	chr1:173683788-173684508	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZBTB33	chr1:173683776-173684277	A549	lung:	n/a	n/a
31	YY1	chr1:173683878-173684632	GM12892	blood:	n/a	n/a
32	POLR2A	chr1:173683844-173684739	Gliobla	brain:	n/a	n/a
33	SIN3AK20	chr1:173683816-173684409	A549	lung:	n/a	n/a
34	E2F6	chr1:173683890-173684544	K562	blood:	n/a	n/a
35	SRF	chr1:173683915-173684174	GM12878	blood:	n/a	n/a
36	STAT3	chr1:173683863-173684208	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr1:173683768-173684769	Hela-S3	cervix:	n/a	n/a
38	MAFF	chr1:173683842-173684156	K562	blood:	n/a	n/a
39	POLR2A	chr1:173683813-173684462	A549	lung:	n/a	n/a
40	SIN3AK20	chr1:173683845-173684311	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr1:173683623-173684767	Hela-S3	cervix:	n/a	n/a
42	MAX	chr1:173683705-173685076	Hela-S3	cervix:	n/a	n/a
43	CHD2	chr1:173683862-173684714	HepG2	liver:	n/a	n/a
44	POLR2A	chr1:173683845-173684620	GM10847	blood:	n/a	n/a
45	POLR2A	chr1:173683918-173684480	HepG2	liver:	n/a	n/a
46	SRF	chr1:173683817-173684237	GM12878	blood:	n/a	n/a
47	MAX	chr1:173683714-173684586	HCT-116	colon:	n/a	n/a
48	MXI1	chr1:173682912-173685311	SK-N-SH	brain:	n/a	n/a
49	FOXA2	chr1:173683785-173684165	HepG2	liver:	n/a	n/a
50	NFIC	chr1:173683752-173684548	ECC-1	luminal epithelium:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:173683938-173683988	HCF	heart:	n/a
2	chr1:173683938-173683988	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:173683938-173683988	PrEC	prostate:	n/a
4	chr1:173683938-173683988	NHDF-neo	bronchial:	n/a
5	chr1:173683938-173683988	HAEpiC	amniotic membrane:	n/a
6	chr1:173683938-173683988	A549	lung:	n/a
7	chr1:173683938-173683988	HCPEpiC	choroid plexus:	n/a
8	chr1:173683938-173683988	BJ	skin:	n/a
9	chr1:173683938-173683988	SK-N-SH_RA	brain:	n/a
10	chr1:173683938-173683988	HRPEpiC	eye:	n/a
11	chr1:173683938-173683988	BE2_C	brain:	n/a
12	chr1:173683938-173683988	Caco-2	colon:	n/a
13	chr1:173683938-173683988	LNCaP	prostate:	n/a
14	chr1:173683938-173683988	CMK	blood:	n/a
15	chr1:173683938-173683988	HIPEpiC	eye:	n/a
16	chr1:173683938-173683988	AoSMC	blood vessel:	n/a
17	chr1:173683938-173683988	MCF10A-Er-Src	breast:	n/a
18	chr1:173683938-173683988	HRCEpiC	kidney:	n/a
19	chr1:173683938-173683988	HMEC	breast:	n/a
20	chr1:173683938-173683988	HCM	heart:	n/a
21	chr1:173683938-173683988	ovcar-3	ovarian:	n/a
22	chr1:173683938-173683988	HCT-116	colon:	n/a
23	chr1:173683938-173683988	H1-hESC	embryonic stem cell:	embryo
24	chr1:173683938-173683988	GM06990	blood:	n/a
25	chr1:173683938-173683988	SAEC	small airway:	n/a
26	chr1:173683938-173683988	HL-60	blood:	n/a
27	chr1:173683938-173683988	AG10803	skin:	n/a
28	chr1:173683938-173683988	NH-A	brain:	n/a
29	chr1:173683938-173683988	MCF-7	breast:	n/a
30	chr1:173683938-173683988	GM19239	blood:	n/a
31	chr1:173683938-173683988	IMR90	lung:	fetal
32	chr1:173683938-173683988	Hela-S3	cervix:	n/a
33	chr1:173683938-173683988	GM12892	blood:	n/a
34	chr1:173683938-173683988	HRE	kidney:	n/a
35	chr1:173683938-173683988	T-47D	breast:	n/a
36	chr1:173683938-173683988	Hepatocyte	liver:	n/a
37	chr1:173683938-173683988	PANC-1	pancreas:	n/a
38	chr1:173683938-173683988	Jurkat	blood:	n/a
39	chr1:173683938-173683988	HEEpiC	esophagus:	n/a
40	chr1:173683938-173683988	AG04450	lung:	fetal
41	chr1:173683938-173683988	GM12891	blood:	n/a
42	chr1:173683938-173683988	AG09319	gingival:	n/a
43	chr1:173683938-173683988	GM12878	blood:	n/a
44	chr1:173683938-173683988	SK-N-SH	brain:	n/a
45	chr1:173683938-173683988	U87	brain:	n/a
46	chr1:173683938-173683988	RPTEC	kidney:	n/a
47	chr1:173683938-173683988	SK-N-MC	brain:	n/a
48	chr1:173683938-173683988	NT2-D1	testis:	n/a
49	chr1:173683938-173683988	ProgFib	skin:	n/a
50	chr1:173683938-173683988	PFSK-1	brain:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173682622..173685584-chr17:56707840..56709510,2	MCF-7	breast:
2	chr1:173445598..173446579-chr1:173683742..173684289,2	Hela-S3	cervix:
3	chr1:173682535..173686916-chr1:173792397..173795534,7	K562	blood:
4	chr1:28974821..28975606-chr1:173683905..173684721,2	Hela-S3	cervix:
5	chr1:173682439..173685635-chr1:173828531..173832401,4	MCF-7	breast:
6	chr1:173683067..173686676-chr1:173791976..173794755,4	K562	blood:
7	chr1:173682287..173685888-chr1:173836010..173838228,4	MCF-7	breast:
8	chr1:173682967..173685869-chr1:173831317..173832954,2	K562	blood:
9	chr1:173446233..173448381-chr1:173683311..173685708,2	MCF-7	breast:

No data

Variant related genes	Relation type
KLHL20	TF binding region
KLHL20	CpG island
ENSG00000270084	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000270103	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10912656	0.91[CHB][hapmap]
rs10912660	0.81[ASN][1000 genomes]
rs10912670	0.84[AMR][1000 genomes]
rs10912671	0.92[ASW][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.84[AMR][1000 genomes]
rs10912676	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12057778	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12071663	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12075071	0.80[ASN][1000 genomes]
rs12086229	0.81[AMR][1000 genomes]
rs12092383	0.85[ASW][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1322770	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1322775	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1322777	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1322780	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap]
rs1799876	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs2144708	0.92[ASW][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap]
rs4606360	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57592568	0.80[ASN][1000 genomes]
rs5877	0.83[ASW][hapmap];0.95[TSI][hapmap]
rs5878	0.83[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap]
rs6413827	0.81[MEX][hapmap]
rs6425254	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6663875	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs7542910	0.82[ASN][1000 genomes]
rs7544605	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7552939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9286895	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs941989	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap]
rs9425430	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs9425745	0.81[MEX][hapmap]
rs9425755	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9425766	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap]
rs9661233	0.82[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv1014827	chr1:173653453-173692470	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10798295	TNFSF18	cis	parietal	SCAN
rs10798295	DARS2	cis	cerebellum	SCAN
rs10798295	GPR52	cis	parietal	SCAN
rs10798295	CENPL	cis	lymphoblastoid	seeQTL
rs10798295	SLC9A11	cis	parietal	SCAN
rs10798295	SNORD78	cis	parietal	SCAN
rs10798295	PRDX6	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173683000-173684000	Flanking Active TSS	Dnd41	blood
2	chr1:173683200-173685400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:173683200-173685400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:173683400-173684000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:173683400-173684000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:173683400-173684000	Flanking Active TSS	Liver	Liver
7	chr1:173683400-173684000	Flanking Active TSS	Hela-S3	cervix
8	chr1:173683400-173684200	Active TSS	Brain Germinal Matrix	brain
9	chr1:173683400-173685000	Active TSS	Brain Substantia Nigra	brain
10	chr1:173683400-173685000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr1:173683400-173685000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr1:173683400-173685200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:173683400-173685200	Active TSS	Brain Hippocampus Middle	brain
14	chr1:173683400-173685200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:173683400-173685200	Active TSS	NHDF-Ad	bronchial
16	chr1:173683400-173685400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:173683400-173685400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:173683400-173685400	Active TSS	NHLF	lung
19	chr1:173683400-173685600	Active TSS	A549	lung
20	chr1:173683400-173685800	Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:173683400-173685800	Active TSS	Stomach Smooth Muscle	stomach
22	chr1:173683400-173686000	Active TSS	K562	blood
23	chr1:173683400-173686600	Active TSS	GM12878-XiMat	blood
24	chr1:173683600-173684000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:173683600-173684000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:173683600-173684000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:173683600-173684000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr1:173683600-173684000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr1:173683600-173684000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr1:173683600-173684000	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr1:173683600-173684000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr1:173683600-173684000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr1:173683600-173684000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr1:173683600-173684000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr1:173683600-173684000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr1:173683600-173684000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:173683600-173684000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:173683600-173684000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr1:173683600-173684000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:173683600-173684000	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr1:173683600-173684000	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr1:173683600-173684000	Enhancers	Gastric	stomach
43	chr1:173683600-173684000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:173683600-173684000	Flanking Active TSS	Stomach Mucosa	stomach
45	chr1:173683600-173684000	Flanking Active TSS	HMEC	breast
46	chr1:173683600-173684000	Flanking Active TSS	HUVEC	blood vessel
47	chr1:173683600-173684000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:173683600-173684000	Flanking Active TSS	NH-A	brain
49	chr1:173683600-173684000	Flanking Active TSS	Osteobl	bone
50	chr1:173683600-173684400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links