Variant report

Variant	rs10031983
Chromosome Location	chr4:76958071-76958072
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr4:76958006-76958261	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr4:76958009-76958302	K562	blood:	n/a	n/a
3	RCOR1	chr4:76958070-76958256	K562	blood:	n/a	n/a
4	YY1	chr4:76958054-76958307	K562	blood:	n/a	n/a
5	YY1	chr4:76957990-76958339	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr4:76958058-76958376	K562	blood:	n/a	n/a
7	CTCF	chr4:76958061-76958354	K562	blood:	n/a	n/a
8	CTCF	chr4:76957941-76958324	K562	blood:	n/a	n/a
9	CTCF	chr4:76958006-76958289	K562	blood:	n/a	n/a
10	YY1	chr4:76957846-76958305	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:76958061-76958111	SK-N-MC	brain:	n/a
2	chr4:76958054-76958104	AG09319	gingival:	n/a
3	chr4:76958061-76958111	GM19239	blood:	n/a
4	chr4:76958061-76958111	NH-A	brain:	n/a
5	chr4:76958054-76958104	HMEC	breast:	n/a
6	chr4:76958061-76958111	T-47D	breast:	n/a
7	chr4:76958054-76958104	MCF-7	breast:	n/a
8	chr4:76958054-76958104	HCPEpiC	choroid plexus:	n/a
9	chr4:76958054-76958104	GM12891	blood:	n/a
10	chr4:76958054-76958104	PFSK-1	brain:	n/a
11	chr4:76958054-76958104	ProgFib	skin:	n/a
12	chr4:76958061-76958111	NHBE	bronchial:	n/a
13	chr4:76958054-76958104	MCF10A-Er-Src	breast:	n/a
14	chr4:76958054-76958104	A549	lung:	n/a
15	chr4:76958054-76958104	SAEC	small airway:	n/a
16	chr4:76958061-76958111	HCT-116	colon:	n/a
17	chr4:76958061-76958111	RPTEC	kidney:	n/a
18	chr4:76958061-76958111	A549	lung:	n/a
19	chr4:76958061-76958111	HepG2	liver:	n/a
20	chr4:76958054-76958104	HCF	heart:	n/a
21	chr4:76958061-76958111	SAEC	small airway:	n/a
22	chr4:76958061-76958111	HMEC	breast:	n/a
23	chr4:76958054-76958104	PANC-1	pancreas:	n/a
24	chr4:76958061-76958111	HEK293	kidney:	embryo
25	chr4:76958054-76958104	CMK	blood:	n/a
26	chr4:76958054-76958104	HAEpiC	amniotic membrane:	n/a
27	chr4:76958061-76958111	NT2-D1	testis:	n/a
28	chr4:76958061-76958111	AG10803	skin:	n/a
29	chr4:76958061-76958111	AG09309	skin:	n/a
30	chr4:76958061-76958111	PANC-1	pancreas:	n/a
31	chr4:76958061-76958111	GM12878	blood:	n/a
32	chr4:76958061-76958111	Hela-S3	cervix:	n/a
33	chr4:76958054-76958104	U87	brain:	n/a
34	chr4:76958054-76958104	AG09309	skin:	n/a
35	chr4:76958054-76958104	AoSMC	blood vessel:	n/a
36	chr4:76958054-76958104	NH-A	brain:	n/a
37	chr4:76958054-76958104	HEEpiC	esophagus:	n/a
38	chr4:76958054-76958104	IMR90	lung:	fetal
39	chr4:76958054-76958104	GM12878	blood:	n/a
40	chr4:76958061-76958111	HCPEpiC	choroid plexus:	n/a
41	chr4:76958054-76958104	AG04449	skin:	fetal
42	chr4:76958061-76958111	HCF	heart:	n/a
43	chr4:76958061-76958111	SK-N-SH_RA	brain:	n/a
44	chr4:76958061-76958111	HIPEpiC	eye:	n/a
45	chr4:76958061-76958111	H1-hESC	embryonic stem cell:	embryo
46	chr4:76958061-76958111	ProgFib	skin:	n/a
47	chr4:76958054-76958104	SK-N-MC	brain:	n/a
48	chr4:76958061-76958111	MCF10A-Er-Src	breast:	n/a
49	chr4:76958054-76958104	HCM	heart:	n/a
50	chr4:76958054-76958104	HPAEpiC	pulmonary alveolar:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76932434..76934325-chr4:76957722..76960530,2	K562	blood:
2	chr4:76956748..76960411-chr4:76960413..76963338,4	K562	blood:

No data

Variant related genes	Relation type
CXCL11	TF binding region
CXCL11	CpG island
ENSG00000156219	Chromatin interaction
ENSG00000169248	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10002977	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10007919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021434	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10029157	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10031733	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10518143	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12374321	0.82[CEU][hapmap]
rs12649185	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651402	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13111494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13118503	0.87[CEU][hapmap]
rs13121161	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13129896	0.81[AMR][1000 genomes]
rs13130917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1394916	1.00[YRI][hapmap]
rs17001247	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs1857821	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs2242470	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2271528	0.87[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs2276886	0.87[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28655366	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2869462	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28818603	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28897072	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34740469	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3733238	0.82[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3796484	0.82[CHB][hapmap]
rs4241577	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4429750	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508917	0.84[EUR][1000 genomes]
rs4859567	0.82[CEU][hapmap]
rs4859571	0.82[CEU][hapmap]
rs4859572	0.80[CHB][hapmap]
rs4859577	0.81[EUR][1000 genomes]
rs4859578	0.93[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs4859580	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs4859609	0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs6841333	0.83[EUR][1000 genomes]
rs6847815	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7688312	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs884004	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9994667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv19222	chr4:76948569-76977780	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1802071	chr4:76948817-76972594	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1815228	chr4:76955027-76959624	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10031983	NAAA	cis	Artery Aorta	GTEx
rs10031983	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs10031983	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs10031983	NAAA	cis	Muscle Skeletal	GTEx
rs10031983	NAAA	cis	Esophagus Mucosa	GTEx
rs10031983	NAAA	cis	Esophagus Muscularis	GTEx
rs10031983	NAAA	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76956800-76958400	Enhancers	HUVEC	blood vessel
2	chr4:76957000-76958200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:76957000-76958400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:76957000-76958400	Enhancers	Pancreas	Pancrea
5	chr4:76957000-76958400	Enhancers	HMEC	breast
6	chr4:76957200-76958200	Enhancers	NHEK	skin
7	chr4:76957200-76958400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:76957200-76958400	Enhancers	K562	blood
9	chr4:76958000-76958200	Enhancers	Right Atrium	heart

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