Variant report

Variant	rs1778214
Chromosome Location	chr1:95061355-95061356
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	STAT3	chr1:95061350-95061535	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:95061330-95061581	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA1	chr1:95061324-95061639	HepG2	liver:	n/a	n/a
4	MAX	chr1:95061339-95061598	Hela-S3	cervix:	n/a	n/a
5	MYC	chr1:95061288-95061642	MCF10A-Er-Src	breast:	n/a	n/a
6	TCF7L2	chr1:95061144-95061672	Hela-S3	cervix:	n/a	n/a
7	FOS	chr1:95061288-95061649	MCF10A-Er-Src	breast:	n/a	chr1:95061369-95061380
8	STAT3	chr1:95061330-95061559	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:95061268-95061602	MCF10A-Er-Src	breast:	n/a	chr1:95061369-95061380
10	EP300	chr1:95061324-95061683	Hela-S3	cervix:	n/a	n/a
11	SMC3	chr1:95061269-95062154	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:95061259-95061407	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr1:95061275-95061688	Hela-S3	cervix:	n/a	n/a
14	STAT3	chr1:95061324-95061588	MCF10A-Er-Src	breast:	n/a	n/a
15	FOXA1	chr1:95061333-95061660	T-47D	breast:	n/a	n/a
16	CEBPB	chr1:95061343-95061661	IMR90	lung:	n/a	n/a
17	RAD21	chr1:95061282-95061623	Hela-S3	cervix:	n/a	n/a
18	FOS	chr1:95061325-95061574	MCF10A-Er-Src	breast:	n/a	chr1:95061369-95061380
19	FOXP2	chr1:95061278-95061547	PFSK-1	brain:	n/a	n/a
20	MYC	chr1:95061275-95061681	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000223675	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11165177	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12092812	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343481	0.87[ASN][1000 genomes]
rs1629015	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747651	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747653	0.99[ASN][1000 genomes]
rs1747654	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747655	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747657	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747659	0.96[ASN][1000 genomes]
rs1772899	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772903	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778211	0.99[ASN][1000 genomes]
rs1778213	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778216	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847313	0.86[ASN][1000 genomes]
rs841709	0.96[ASN][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	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv871279	chr1:95028981-95083836	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1804937	chr1:95051930-95081587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95046000-95065400	Weak transcription	Fetal Intestine Large	intestine
2	chr1:95055000-95061400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:95055000-95061600	Enhancers	Brain Anterior Caudate	brain
4	chr1:95055000-95062000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:95055400-95061800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:95056200-95067800	Weak transcription	Gastric	stomach
7	chr1:95056400-95061400	Weak transcription	Fetal Lung	lung
8	chr1:95056800-95069000	Weak transcription	Right Atrium	heart
9	chr1:95057000-95061600	Enhancers	Brain Hippocampus Middle	brain
10	chr1:95057400-95069000	Weak transcription	Aorta	Aorta
11	chr1:95057800-95061400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:95059000-95061400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:95059200-95061600	Weak transcription	Brain Germinal Matrix	brain
14	chr1:95059200-95062800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:95059400-95064600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:95059400-95074200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:95060200-95062400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:95060400-95061600	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:95060400-95063000	Weak transcription	Hela-S3	cervix
20	chr1:95060600-95061600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:95060600-95061600	Enhancers	NHEK	skin
22	chr1:95060600-95062000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:95060600-95062000	Enhancers	Fetal Muscle Leg	muscle
24	chr1:95060800-95061400	Weak transcription	Brain Angular Gyrus	brain
25	chr1:95060800-95061800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:95060800-95063400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:95060800-95064400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:95060800-95065400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:95061000-95061800	Enhancers	Fetal Intestine Small	intestine
30	chr1:95061000-95062000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:95061000-95062000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:95061200-95061400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:95061200-95061400	Enhancers	Brain Substantia Nigra	brain
34	chr1:95061200-95061600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr1:95061200-95061600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:95061200-95061600	Weak transcription	Placenta	Placenta
37	chr1:95061200-95061600	Enhancers	Stomach Mucosa	stomach
38	chr1:95061200-95061600	Enhancers	HMEC	breast
39	chr1:95061200-95061600	Enhancers	NHLF	lung
40	chr1:95061200-95061800	Bivalent Enhancer	HepG2	liver
41	chr1:95061200-95062000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links