Variant report

Variant	rs954050
Chromosome Location	chr7:97880226-97880227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:97880192-97880512	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:97880126-97880417	GM12878	blood:	n/a	n/a
3	CTCF	chr7:97880215-97880383	GM19239	blood:	n/a	n/a
4	CTCF	chr7:97880220-97880370	GM12869	blood:	n/a	n/a
5	MXI1	chr7:97880195-97880447	GM12878	blood:	n/a	n/a
6	CTCF	chr7:97880200-97880350	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr7:97880107-97880545	K562	blood:	n/a	n/a
8	JUND	chr7:97880194-97880453	K562	blood:	n/a	n/a
9	MYC	chr7:97880212-97880410	K562	blood:	n/a	n/a
10	CTCF	chr7:97880200-97880350	GM12864	blood:	n/a	n/a
11	FOXA1	chr7:97879975-97880462	HepG2	liver:	n/a	n/a
12	WRNIP1	chr7:97880120-97880511	GM12878	blood:	n/a	n/a
13	CTCF	chr7:97880180-97880330	SAEC	small airway:	n/a	n/a
14	YY1	chr7:97880199-97880339	K562	blood:	n/a	n/a
15	GABPA	chr7:97880123-97880403	K562	blood:	n/a	n/a
16	POLR2A	chr7:97880225-97881989	GM18951	blood:	n/a	n/a
17	CTCF	chr7:97880220-97880370	A549	lung:	n/a	n/a
18	CTCF	chr7:97880213-97880389	GM12878	blood:	n/a	n/a
19	CHD2	chr7:97880174-97880427	GM12878	blood:	n/a	n/a
20	CTCF	chr7:97880211-97880404	GM12891	blood:	n/a	n/a
21	RAD21	chr7:97880204-97880365	K562	blood:	n/a	n/a
22	SIN3A	chr7:97880210-97882216	H1-hESC	embryonic stem cell:	n/a	chr7:97880924-97880935
23	RCOR1	chr7:97880108-97880327	GM12878	blood:	n/a	n/a
24	TBL1XR1	chr7:97880039-97880400	GM12878	blood:	n/a	n/a
25	RUNX3	chr7:97880112-97880411	GM12878	blood:	n/a	n/a
26	CTCF	chr7:97880100-97880250	GM12866	blood:	n/a	n/a
27	GABPA	chr7:97880112-97880353	K562	blood:	n/a	n/a
28	FOXA1	chr7:97880014-97880443	HepG2	liver:	n/a	n/a
29	GABPA	chr7:97880090-97880336	HepG2	liver:	n/a	n/a
30	RFX5	chr7:97880210-97880280	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:97880021-97880452	GM12892	blood:	n/a	n/a
32	NR2F2	chr7:97880125-97880522	K562	blood:	n/a	n/a
33	CTCF	chr7:97880178-97880379	K562	blood:	n/a	n/a
34	CTCF	chr7:97880177-97880506	K562	blood:	n/a	n/a
35	CTCF	chr7:97880200-97880350	MCF-7	breast:	n/a	n/a
36	POLR2A	chr7:97880144-97880740	HUVEC	blood vessel:	n/a	n/a
37	CTCF	chr7:97880201-97880424	GM12892	blood:	n/a	n/a
38	CTCF	chr7:97880200-97880350	GM12878	blood:	n/a	n/a
39	EBF1	chr7:97880225-97880361	GM12878	blood:	n/a	n/a
40	POLR2A	chr7:97880156-97880406	GM12878	blood:	n/a	n/a
41	POLR2A	chr7:97880131-97882153	GM12878	blood:	n/a	n/a
42	FOXA2	chr7:97880100-97880307	HepG2	liver:	n/a	n/a
43	CTCF	chr7:97880207-97880415	GM19238	blood:	n/a	n/a
44	POLR2A	chr7:97880009-97880896	GM12892	blood:	n/a	n/a
45	MAFK	chr7:97880061-97880278	HepG2	liver:	n/a	n/a
46	HEY1	chr7:97880047-97880501	HepG2	liver:	n/a	n/a
47	POLR2A	chr7:97880155-97882023	GM19193	blood:	n/a	n/a
48	MTA3	chr7:97880209-97880577	GM12878	blood:	n/a	n/a
49	FOXA1	chr7:97880000-97880458	HepG2	liver:	n/a	n/a
50	CREB1	chr7:97879961-97880505	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97847018..97848537-chr7:97878984..97881844,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BAIAP2L1.1-1	chr7:97880226-97880860	NONHSAT122185

No data

Variant related genes	Relation type
TECPR1	TF binding region
BRI3	TF binding region
ENSG00000205356	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10249366	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10953247	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10953256	0.82[CHB][hapmap]
rs10953257	0.82[CHB][hapmap]
rs1132971	0.82[CHB][hapmap]
rs11761574	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11771397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11771953	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11772438	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11773779	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11984183	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533016	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12539676	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12669622	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12704981	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12704983	0.82[CHB][hapmap]
rs12728	0.82[CHB][hapmap]
rs13232181	0.82[CHB][hapmap]
rs1468338	0.82[CHB][hapmap]
rs17436977	0.88[CHB][hapmap]
rs1859482	0.82[CHB][hapmap]
rs2107716	0.82[CHB][hapmap]
rs2270600	0.89[EUR][1000 genomes]
rs2270604	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286074	0.82[CHB][hapmap]
rs2291747	0.85[CEU][hapmap]
rs2394827	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28566958	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28662014	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3801255	0.82[CHB][hapmap]
rs3801256	0.82[CHB][hapmap]
rs3801263	0.82[CHB][hapmap]
rs3801264	0.82[CHB][hapmap]
rs3823740	0.82[CHB][hapmap]
rs4727388	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4727390	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4729421	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56098787	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61575270	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62479836	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62479838	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6465664	0.81[CHB][hapmap]
rs6465666	0.82[CHB][hapmap]
rs6465667	0.82[CHB][hapmap]
rs6465672	0.82[CHB][hapmap]
rs6465675	0.82[CHB][hapmap]
rs6465680	0.80[CEU][hapmap]
rs6945554	0.82[CHB][hapmap]
rs6947340	0.82[CHB][hapmap]
rs6948540	0.82[CHB][hapmap]
rs6949718	0.81[CHB][hapmap]
rs6951479	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6955647	0.81[CHB][hapmap]
rs6961129	0.88[CHB][hapmap]
rs6963210	0.82[CHB][hapmap]
rs6968193	0.82[CHB][hapmap]
rs6970801	0.82[CHB][hapmap]
rs6970990	0.82[CHB][hapmap]
rs6975156	0.81[CHB][hapmap]
rs736753	0.82[CHB][hapmap]
rs7458551	0.82[CHB][hapmap]
rs747631	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747632	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7776638	0.81[CHB][hapmap]
rs7777415	0.82[CHB][hapmap]
rs7781916	0.82[CHB][hapmap]
rs7787309	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7789380	0.82[CHB][hapmap]
rs7796762	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs7797943	0.82[CHB][hapmap]
rs7807455	0.82[CHB][hapmap]
rs7807555	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS 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 miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer 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	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription 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	10 gene(s)	inside rSNPs	diseases
9	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1800947	chr7:97857675-97889672	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers 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	19 gene(s)	inside rSNPs	diseases
14	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs954050	TECPR1	cis	parietal	SCAN
rs954050	FIS1	cis	parietal	SCAN
rs954050	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs954050	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL
rs954050	GATS	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97848000-97880600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:97866000-97880400	Weak transcription	Fetal Kidney	kidney
3	chr7:97869000-97880600	Weak transcription	NH-A	brain
4	chr7:97871800-97880400	Weak transcription	Osteobl	bone
5	chr7:97874000-97880800	Weak transcription	Ovary	ovary
6	chr7:97874200-97881000	Weak transcription	Aorta	Aorta
7	chr7:97877200-97880800	Enhancers	Spleen	Spleen
8	chr7:97877400-97880600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr7:97877400-97880600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr7:97877600-97880400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:97877600-97880600	Enhancers	Primary hematopoietic stem cells	blood
12	chr7:97877600-97880600	Weak transcription	Left Ventricle	heart
13	chr7:97877800-97880400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:97877800-97880800	Weak transcription	Lung	lung
15	chr7:97878000-97880400	Enhancers	Small Intestine	intestine
16	chr7:97878200-97880400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:97878200-97880400	Enhancers	Stomach Mucosa	stomach
18	chr7:97878200-97880600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr7:97879000-97880400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:97879200-97880600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr7:97879200-97881000	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr7:97879400-97880400	Enhancers	Fetal Brain Male	brain
23	chr7:97879400-97880600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr7:97879400-97880800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr7:97879400-97881200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr7:97879600-97880400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:97879600-97880600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr7:97879600-97880600	Enhancers	Fetal Muscle Leg	muscle
29	chr7:97879800-97880600	Enhancers	Fetal Muscle Trunk	muscle
30	chr7:97879800-97881000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr7:97879800-97881000	Flanking Active TSS	Dnd41	blood
32	chr7:97879800-97881200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr7:97879800-97881200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr7:97879800-97881200	Flanking Active TSS	GM12878-XiMat	blood
35	chr7:97880000-97880400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:97880000-97880400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:97880000-97880400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:97880000-97880400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:97880000-97880400	Enhancers	Brain Hippocampus Middle	brain
40	chr7:97880000-97880400	Enhancers	Right Ventricle	heart
41	chr7:97880000-97880400	Active TSS	Stomach Smooth Muscle	stomach
42	chr7:97880000-97880600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr7:97880000-97880600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr7:97880000-97880600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr7:97880000-97880600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:97880000-97880600	Enhancers	Brain Angular Gyrus	brain
47	chr7:97880000-97880600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr7:97880000-97880600	Enhancers	Fetal Lung	lung
49	chr7:97880000-97880600	Enhancers	Placenta	Placenta
50	chr7:97880000-97880600	Flanking Active TSS	Thymus	Thymus

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