Variant report

Variant	rs10046397
Chromosome Location	chr6:37880013-37880014
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	CEBPB	chr6:37880000-37880203	HepG2	liver:	n/a	chr6:37880087-37880098
2	POLR2A	chr6:37879998-37880060	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37873838..37876151-chr6:37878592..37881455,2	K562	blood:

Variant related genes	Relation type
RNU1-87P	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10080245	1.00[EUR][1000 genomes]
rs11961284	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs12178911	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55933649	1.00[EUR][1000 genomes]
rs56958593	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57527781	0.92[AFR][1000 genomes]
rs58305294	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58698408	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58860274	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60774419	1.00[EUR][1000 genomes]
rs60997161	1.00[EUR][1000 genomes]
rs6904932	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6906120	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6912045	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6917912	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs6918445	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6924117	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6926669	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730817	0.80[AFR][1000 genomes]
rs73730818	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730823	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730827	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73730832	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730849	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730859	1.00[EUR][1000 genomes]
rs73730877	1.00[EUR][1000 genomes]
rs73730883	1.00[EUR][1000 genomes]
rs7756841	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7765448	1.00[EUR][1000 genomes]
rs7769848	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7770297	1.00[EUR][1000 genomes]
rs7773080	0.92[YRI][hapmap]
rs9296235	1.00[YRI][hapmap]
rs9462362	1.00[EUR][1000 genomes]
rs9462367	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9462370	1.00[EUR][1000 genomes]
rs9462371	1.00[EUR][1000 genomes]
rs9462375	1.00[EUR][1000 genomes]
rs9470711	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470715	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470716	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470717	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9470719	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470722	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470729	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470731	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470733	1.00[EUR][1000 genomes]
rs9470736	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470744	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470745	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470757	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9470766	1.00[EUR][1000 genomes]
rs9470770	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9470771	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs9470774	0.92[YRI][hapmap]
rs9470781	1.00[YRI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv970036	chr6:37876765-37894762	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37850600-37890400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37851000-37884600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:37857600-37886000	Weak transcription	Esophagus	oesophagus
4	chr6:37857600-37895400	Weak transcription	Pancreas	Pancrea
5	chr6:37862400-37884000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:37862600-37882000	Weak transcription	Fetal Intestine Small	intestine
7	chr6:37864600-37880800	Weak transcription	NHDF-Ad	bronchial
8	chr6:37866000-37885600	Weak transcription	Hela-S3	cervix
9	chr6:37872000-37887600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:37872000-37888200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:37872000-37890400	Weak transcription	Small Intestine	intestine
12	chr6:37872200-37883000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:37872200-37884000	Weak transcription	Adipose Nuclei	Adipose
14	chr6:37872200-37884600	Weak transcription	Fetal Kidney	kidney
15	chr6:37872400-37883000	Weak transcription	Brain Substantia Nigra	brain
16	chr6:37872600-37885200	Weak transcription	HepG2	liver
17	chr6:37872600-37896400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:37872800-37880600	Weak transcription	HMEC	breast
19	chr6:37872800-37880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:37873000-37882600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:37873200-37887400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:37874000-37888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:37874200-37884600	Weak transcription	A549	lung
25	chr6:37874400-37880800	Weak transcription	Osteobl	bone
26	chr6:37874400-37887600	Weak transcription	Spleen	Spleen
27	chr6:37874400-37888200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:37874600-37880400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:37874600-37903800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:37874800-37881600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:37875000-37880600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:37875400-37880200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:37876000-37880800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:37876600-37880400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr6:37876600-37903200	Weak transcription	Dnd41	blood
36	chr6:37877400-37880800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:37877600-37882800	Weak transcription	Liver	Liver
38	chr6:37877600-37884000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:37877800-37881400	Enhancers	Primary T cells from cord blood	blood
40	chr6:37877800-37881800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:37878000-37883200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:37878000-37883200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:37878200-37883400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:37878200-37883800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:37878400-37880200	Enhancers	Colon Smooth Muscle	Colon
46	chr6:37878800-37881200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr6:37878800-37900400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:37879600-37880200	Enhancers	Thymus	Thymus
49	chr6:37879600-37882600	Weak transcription	Fetal Heart	heart
50	chr6:37879600-37889600	Weak transcription	K562	blood

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