Variant report

Variant	rs3808077
Chromosome Location	chr7:127584326-127584327
allele	A/T
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	NFIC	chr7:127583926-127584641	ECC-1	luminal epithelium:	n/a	chr7:127584294-127584311 chr7:127584294-127584310
2	POLR2A	chr7:127584071-127584651	K562	blood:	n/a	n/a
3	POLR2A	chr7:127583827-127584460	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr7:127584012-127584811	K562	blood:	n/a	n/a
5	NFIC	chr7:127583992-127584581	ECC-1	luminal epithelium:	n/a	chr7:127584294-127584311 chr7:127584294-127584310
6	POLR2A	chr7:127583911-127584530	K562	blood:	n/a	n/a
7	POLR2A	chr7:127584305-127584593	K562	blood:	n/a	n/a
8	NFIC	chr7:127584042-127584624	SK-N-SH	brain:	n/a	chr7:127584294-127584311 chr7:127584294-127584310

Variant related genes	Relation type
SND1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1024910	0.82[ASN][1000 genomes]
rs1193333	0.83[ASN][1000 genomes]
rs1193335	0.82[ASN][1000 genomes]
rs1193336	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12668077	0.94[JPT][hapmap]
rs1345509	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419968	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17732677	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs178734	0.82[ASN][1000 genomes]
rs2241291	0.81[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs225241	0.82[ASN][1000 genomes]
rs322826	0.81[CHB][hapmap]
rs322827	0.88[JPT][hapmap]
rs322828	0.88[JPT][hapmap]
rs322834	0.82[ASN][1000 genomes]
rs35774036	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757755	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3757760	0.81[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3757763	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs3779526	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779527	0.81[ASN][1000 genomes]
rs3808056	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs3808061	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808082	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808088	0.94[JPT][hapmap]
rs3823995	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4731386	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467155	0.82[ASN][1000 genomes]
rs6467156	0.82[ASN][1000 genomes]
rs6944446	0.87[JPT][hapmap]
rs6973092	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7789322	0.82[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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127562200-127589800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:127568200-127594000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:127569800-127615600	Weak transcription	Colonic Mucosa	Colon
4	chr7:127570000-127585800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:127570000-127591400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:127570600-127584600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:127570600-127615600	Weak transcription	Small Intestine	intestine
8	chr7:127570600-127615800	Weak transcription	Esophagus	oesophagus
9	chr7:127570600-127616400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr7:127570800-127589200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:127570800-127599600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr7:127570800-127618200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr7:127571000-127615600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr7:127571000-127615800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:127571400-127589800	Weak transcription	Fetal Stomach	stomach
16	chr7:127571400-127617800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr7:127571600-127584800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:127571600-127594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr7:127571600-127618000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:127571800-127602800	Weak transcription	Aorta	Aorta
21	chr7:127573200-127588600	Weak transcription	Ovary	ovary
22	chr7:127574400-127587600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:127576400-127589000	Weak transcription	Fetal Kidney	kidney
24	chr7:127576400-127607000	Weak transcription	Spleen	Spleen
25	chr7:127576400-127615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:127577400-127588000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:127577800-127584800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:127577800-127585000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:127577800-127585200	Strong transcription	Primary T cells from cord blood	blood
30	chr7:127577800-127586000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:127577800-127587400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr7:127577800-127588000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr7:127578000-127585800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr7:127578000-127588400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:127578000-127588800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:127578000-127588800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr7:127578200-127616200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr7:127578800-127600200	Weak transcription	Stomach Mucosa	stomach
39	chr7:127579200-127586400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:127579400-127586000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:127579400-127592600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:127579800-127585600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:127580200-127585200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:127580400-127588000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:127581000-127588000	Strong transcription	Liver	Liver
46	chr7:127581000-127588600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:127581000-127594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:127581200-127587800	Weak transcription	Fetal Intestine Large	intestine
49	chr7:127581200-127615400	Weak transcription	Gastric	stomach
50	chr7:127581800-127586000	Weak transcription	NHDF-Ad	bronchial

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