Variant report

Variant	rs12663985
Chromosome Location	chr6:45643875-45643876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45643267..45645325-chr6:45679837..45682530,2	MCF-7	breast:
2	chr6:45387873..45391350-chr6:45642901..45646664,5	MCF-7	breast:
3	chr6:45386304..45389959-chr6:45643687..45645408,3	MCF-7	breast:
4	chr6:45574169..45577727-chr6:45643786..45647502,3	MCF-7	breast:
5	chr6:45643355..45645914-chr6:45665891..45668541,2	MCF-7	breast:
6	chr6:45643425..45645102-chr6:45658763..45660463,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271857	Chromatin interaction
ENSG00000124813	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12175323	0.98[ASN][1000 genomes]
rs12661654	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12665728	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1388242	0.95[JPT][hapmap]
rs1388244	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1491139	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1491144	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491145	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1994682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035791	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2396505	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs321321	0.81[CEU][hapmap]
rs321324	0.94[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs321325	0.94[CEU][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4326224	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4714863	0.82[ASN][1000 genomes]
rs4714864	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458457	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6458458	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7761790	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7762915	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7774097	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349322	0.92[ASN][1000 genomes]
rs9349323	0.82[ASN][1000 genomes]
rs9349324	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9357489	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9369572	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9395110	0.86[ASN][1000 genomes]
rs9395111	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9472541	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9472547	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9472548	0.98[ASN][1000 genomes]
rs9472552	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9472557	0.94[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45631800-45645000	Weak transcription	Colonic Mucosa	Colon
2	chr6:45634200-45645200	Weak transcription	Right Atrium	heart
3	chr6:45635000-45644800	Weak transcription	NHLF	lung
4	chr6:45635600-45644200	Weak transcription	HSMM	muscle
5	chr6:45635600-45644800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:45642200-45646400	Enhancers	Fetal Thymus	thymus
7	chr6:45643000-45644200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr6:45643000-45644800	Enhancers	Primary T cells from cord blood	blood
9	chr6:45643000-45644800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:45643000-45645000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr6:45643000-45645000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:45643000-45645000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:45643000-45646000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:45643200-45644200	Enhancers	Pancreas	Pancrea
15	chr6:45643200-45644800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr6:45643200-45644800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr6:45643200-45644800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:45643200-45644800	Enhancers	Dnd41	blood
19	chr6:45643200-45645000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:45643200-45645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:45643200-45645200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:45643200-45646000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:45643400-45644000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:45643400-45644800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:45643400-45644800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:45643400-45645200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:45643400-45647600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:45643400-45647800	Enhancers	Primary B cells from peripheral blood	blood
29	chr6:45643600-45644800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:45643600-45644800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:45643600-45644800	Weak transcription	NHEK	skin
32	chr6:45643600-45645000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:45643600-45645000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:45643600-45645000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:45643600-45645000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr6:45643600-45645000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:45643800-45644000	Enhancers	Brain Hippocampus Middle	brain
38	chr6:45643800-45644800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:45643800-45644800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:45643800-45644800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:45643800-45645000	Weak transcription	Esophagus	oesophagus
42	chr6:45643800-45645000	Weak transcription	Gastric	stomach
43	chr6:45643800-45645000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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