Variant report

Variant	rs7760221
Chromosome Location	chr6:24880090-24880091
allele	C/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	POLR2A	chr6:24879382-24880400	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:24879694-24880142	Hela-S3	cervix:	n/a	n/a
3	GATA3	chr6:24879507-24880101	SK-N-SH	brain:	n/a	n/a
4	STAT1	chr6:24879456-24880165	Hela-S3	cervix:	n/a	chr6:24879895-24879907 chr6:24880076-24880090
5	POLR2A	chr6:24879435-24880133	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
FAM65B	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10946732	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946734	0.84[YRI][hapmap]
rs10946735	0.87[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12110774	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12111413	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192978	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211772	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215106	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220782	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17671350	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207400	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2207401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747679	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28385634	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35158242	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35250553	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35953835	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61595405	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456637	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918387	0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918511	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555168	0.98[EUR][1000 genomes];1.00[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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3507963	chr6:24878423-24880421	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24855200-24895000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
2	chr6:24856200-24882400	Weak transcription	NHLF	lung
3	chr6:24859400-24886800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:24862800-24885600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr6:24862800-24887400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:24870400-24883800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr6:24871800-24886800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:24874800-24883200	Weak transcription	Brain Anterior Caudate	brain
9	chr6:24874800-24883600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:24875400-24882000	Weak transcription	NHDF-Ad	bronchial
11	chr6:24875600-24886800	Weak transcription	Fetal Heart	heart
12	chr6:24875800-24887800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
14	chr6:24876200-24882600	Weak transcription	HSMMtube	muscle
15	chr6:24876600-24880800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:24876800-24880600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr6:24877000-24883000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:24877000-24888000	Genic enhancers	Primary T cells from cord blood	blood
19	chr6:24877200-24880400	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr6:24877400-24883400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:24877400-24888000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:24877600-24880200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:24877600-24881400	Weak transcription	Psoas Muscle	Psoas
24	chr6:24877800-24882000	Strong transcription	Primary B cells from cord blood	blood
25	chr6:24878000-24880200	Enhancers	Placenta	Placenta
26	chr6:24878200-24880200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:24878400-24881200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:24878400-24881800	Weak transcription	Fetal Thymus	thymus
29	chr6:24878400-24884000	Weak transcription	Esophagus	oesophagus
30	chr6:24878400-24887800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr6:24878400-24899800	Weak transcription	Thymus	Thymus
32	chr6:24878600-24882200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:24878800-24885400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr6:24879000-24880800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr6:24879000-24881000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:24879200-24880600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:24879200-24888200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:24879400-24880200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:24879400-24880200	Flanking Active TSS	Hela-S3	cervix
40	chr6:24879400-24880600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:24879400-24882800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:24879400-24883200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:24879600-24880200	Enhancers	Osteobl	bone
44	chr6:24879600-24880600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr6:24879600-24880600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr6:24879600-24880600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr6:24879600-24880600	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr6:24879600-24881000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:24879800-24880200	Enhancers	H9 Cell Line	embryonic stem cell
50	chr6:24879800-24880200	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links