Variant report

Variant	rs10097659
Chromosome Location	chr8:8241316-8241317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:8241189-8244122	GM12891	blood:	n/a	n/a
2	CTCF	chr8:8241255-8241338	A549	lung:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
3	SMC3	chr8:8241158-8241410	GM12878	blood:	n/a	chr8:8241286-8241300
4	CTCF	chr8:8241220-8241370	AG04449	skin:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
5	CTCF	chr8:8241260-8241410	GM12872	blood:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
6	CTCF	chr8:8241240-8241390	HMF	breast:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
7	CTCF	chr8:8241209-8241355	A549	lung:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
8	CTCF	chr8:8241280-8241316	ProgFib	skin:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
9	ETS1	chr8:8241106-8241678	A549	lung:	n/a	chr8:8241651-8241662 chr8:8241655-8241662 chr8:8241408-8241415
10	CTCF	chr8:8241185-8241357	T-47D	breast:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
11	CTCF	chr8:8241238-8241334	GM20000	blood:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
12	CTCF	chr8:8241232-8241328	LNCaP	prostate:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
13	RAD21	chr8:8241098-8241540	SK-N-SH_RA	brain:	n/a	chr8:8241285-8241304
14	RAD21	chr8:8241022-8241613	A549	lung:	n/a	chr8:8241285-8241304
15	CTCF	chr8:8241280-8241430	HBMEC	blood vessel:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
16	CTCF	chr8:8241220-8241370	Caco-2	colon:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
17	RAD21	chr8:8241076-8241472	HepG2	liver:	n/a	chr8:8241285-8241304
18	TCF12	chr8:8241054-8242086	A549	lung:	n/a	n/a
19	CTCF	chr8:8241260-8241410	HAc	cerebellar:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
20	CTCF	chr8:8241280-8241430	RPTEC	kidney:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
21	CTCF	chr8:8241240-8241390	HFF	foreskin:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
22	CTCF	chr8:8241240-8241390	AG10803	skin:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
23	CTCF	chr8:8241232-8241344	GM10266	blood:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
24	CTCF	chr8:8241220-8241370	HRPEpiC	eye:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
25	CTCF	chr8:8241220-8241370	MCF-7	breast:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
26	RAD21	chr8:8241173-8241556	MCF-7	breast:	n/a	chr8:8241285-8241304
27	RAD21	chr8:8241126-8241655	MCF-7	breast:	n/a	chr8:8241285-8241304
28	CTCF	chr8:8241220-8241370	RPTEC	kidney:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
29	POLR2A	chr8:8241285-8242041	GM12892	blood:	n/a	n/a
30	CTCF	chr8:8241200-8241350	HCPEpiC	choroid plexus:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
31	CTCF	chr8:8241280-8241430	GM12864	blood:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
32	RAD21	chr8:8241179-8241453	HepG2	liver:	n/a	chr8:8241285-8241304
33	CTCF	chr8:8241180-8241330	HPAF	blood vessel:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
34	CTCF	chr8:8241240-8241390	HPAF	blood vessel:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
35	CTCF	chr8:8241224-8241377	HepG2	liver:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
36	CTCF	chr8:8241240-8241390	AG09309	skin:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
37	RAD21	chr8:8241081-8241575	H1-hESC	embryonic stem cell:	n/a	chr8:8241285-8241304
38	CTCF	chr8:8241300-8241450	HFF-Myc	foreskin:	n/a	n/a
39	CTCF	chr8:8241191-8241432	H1-hESC	embryonic stem cell:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
40	ZNF143	chr8:8241150-8241446	GM12878	blood:	n/a	n/a
41	CTCF	chr8:8241243-8241328	SK-N-SH_RA	brain:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
42	CTCF	chr8:8241218-8241376	GM12878	blood:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
43	POLR2A	chr8:8238700-8244933	HepG2	liver:	n/a	n/a
44	REST	chr8:8241245-8241833	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr8:8241176-8242517	GM12878	blood:	n/a	n/a
46	RAD21	chr8:8241200-8241462	HepG2	liver:	n/a	chr8:8241285-8241304
47	CTCF	chr8:8241220-8241370	HPF	lung:	n/a	chr8:8241284-8241302 chr8:8241286-8241307
48	CTCF	chr8:8241300-8241450	HCM	heart:	n/a	n/a
49	SMC3	chr8:8241140-8241443	Hela-S3	cervix:	n/a	chr8:8241286-8241300
50	CTCF	chr8:8241220-8241370	HCPEpiC	choroid plexus:	n/a	chr8:8241284-8241302 chr8:8241286-8241307

No.	Distal block	Cell Line	Cell type
1	chr8:8108549..8111183-chr8:8240516..8242778,2	MCF-7	breast:
2	chr8:8235042..8240063-chr8:8240771..8244973,7	MCF-7	breast:
3	chr8:8239788..8242444-chr8:8287010..8288532,2	MCF-7	breast:
4	chr8:8233939..8236566-chr8:8240658..8243964,3	K562	blood:
5	chr8:8241176..8241736-chr8:8524635..8525188,2	MCF-7	breast:
6	chr8:8240498..8242072-chr8:8280467..8282099,2	MCF-7	breast:
7	chr8:8240682..8243465-chr8:8266165..8269097,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182319	TF binding region
ENSG00000182319	Chromatin interaction
ENSG00000253505	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10089767	0.93[CHB][hapmap]
rs10216498	0.91[EUR][1000 genomes]
rs3932318	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs4240617	0.86[CEU][hapmap];0.80[GIH][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4840341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840952	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817196	chr8:8079861-8255544	Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv465448	chr8:8098079-8403142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv610152	chr8:8098079-8403142	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv610154	chr8:8101641-8328101	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1032259	chr8:8108863-8247113	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1020290	chr8:8108863-8260280	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv539440	chr8:8108863-8260280	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1029268	chr8:8130629-8403435	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv539446	chr8:8130629-8403435	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers 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
15	nsv831227	chr8:8204838-8367160	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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	21 gene(s)	inside rSNPs	diseases
17	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
18	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10097659	ERI1	cis	parietal	SCAN
rs10097659	CTSB	cis	cerebellum	SCAN
rs10097659	MTMR9	cis	parietal	SCAN
rs10097659	DEFB134	cis	cerebellum	SCAN
rs10097659	SGK223	cis	parietal	SCAN
rs10097659	C8orf12	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8220400-8241800	Weak transcription	NHDF-Ad	bronchial
2	chr8:8230200-8241600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:8234000-8241400	Weak transcription	Hela-S3	cervix
4	chr8:8235000-8241600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr8:8235600-8241400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr8:8236000-8241400	Weak transcription	Gastric	stomach
7	chr8:8236000-8241400	Weak transcription	Ovary	ovary
8	chr8:8236200-8242600	Weak transcription	Aorta	Aorta
9	chr8:8237400-8241400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:8237400-8241400	Weak transcription	Brain Hippocampus Middle	brain
11	chr8:8237400-8241400	Weak transcription	Esophagus	oesophagus
12	chr8:8237400-8241800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr8:8237400-8242200	Weak transcription	Liver	Liver
14	chr8:8238200-8241400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr8:8238400-8241400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr8:8238600-8241400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr8:8238800-8241800	Transcr. at gene 5' and 3'	A549	lung
18	chr8:8238800-8243400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr8:8239200-8241400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr8:8239200-8241400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr8:8239200-8241400	Weak transcription	Pancreas	Pancrea
22	chr8:8239200-8243000	Weak transcription	Spleen	Spleen
23	chr8:8239400-8241400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr8:8239400-8241400	Weak transcription	Colonic Mucosa	Colon
25	chr8:8239400-8241400	Weak transcription	Lung	lung
26	chr8:8239600-8241400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr8:8239800-8241400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr8:8239800-8241400	Enhancers	Fetal Intestine Small	intestine
29	chr8:8239800-8241600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
30	chr8:8239800-8242000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr8:8240000-8241600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr8:8240200-8241400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr8:8240200-8241400	Active TSS	Fetal Brain Female	brain
34	chr8:8240200-8241400	Weak transcription	HSMM	muscle
35	chr8:8240400-8241400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr8:8240400-8241400	Active TSS	Adipose Nuclei	Adipose
37	chr8:8240400-8241400	Enhancers	Dnd41	blood
38	chr8:8240600-8241400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr8:8240600-8241600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr8:8240800-8241400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr8:8240800-8241400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr8:8240800-8241400	Active TSS	HepG2	liver
43	chr8:8240800-8241600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr8:8240800-8241600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr8:8240800-8242000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr8:8240800-8242400	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr8:8241000-8241400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr8:8241000-8241400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr8:8241000-8241400	Enhancers	Fetal Brain Male	brain
50	chr8:8241000-8241400	Enhancers	Fetal Kidney	kidney

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