Variant report

Variant	rs12178630
Chromosome Location	chr6:144646232-144646233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144641871..144646816-chr6:144650336..144652619,4	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11970041	0.91[AMR][1000 genomes]
rs17073670	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2223428	1.00[AMR][1000 genomes]
rs2328570	1.00[AMR][1000 genomes]
rs28737224	0.91[AMR][1000 genomes]
rs6570620	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570621	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6902637	0.91[AMR][1000 genomes]
rs6905106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932679	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9321971	1.00[AMR][1000 genomes]
rs9484865	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484866	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484867	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484868	1.00[AMR][1000 genomes]
rs9484869	0.91[AMR][1000 genomes]
rs9484870	0.91[AMR][1000 genomes]
rs9496924	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496929	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496933	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9496934	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9496939	1.00[AMR][1000 genomes]
rs9496940	1.00[AMR][1000 genomes]
rs9496941	1.00[AMR][1000 genomes]
rs9496942	1.00[AMR][1000 genomes]
rs9496946	1.00[AMR][1000 genomes]
rs9496947	0.91[AMR][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	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144616400-144648000	Weak transcription	NHEK	skin
2	chr6:144624400-144648000	Weak transcription	HMEC	breast
3	chr6:144630200-144648400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:144630600-144648200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:144635000-144651000	Weak transcription	Small Intestine	intestine
6	chr6:144635600-144650800	Weak transcription	Aorta	Aorta
7	chr6:144636000-144656200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:144636600-144648000	Weak transcription	Brain Anterior Caudate	brain
9	chr6:144636600-144654800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:144636800-144650800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:144636800-144654800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:144636800-144656400	Weak transcription	Brain Substantia Nigra	brain
13	chr6:144637000-144647600	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:144637000-144651800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:144637200-144647800	Weak transcription	Left Ventricle	heart
16	chr6:144637200-144647800	Weak transcription	Right Atrium	heart
17	chr6:144637200-144648000	Weak transcription	Psoas Muscle	Psoas
18	chr6:144637400-144647800	Weak transcription	Fetal Stomach	stomach
19	chr6:144637400-144648400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:144637600-144647800	Weak transcription	Right Ventricle	heart
21	chr6:144639600-144660200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:144641200-144648000	Weak transcription	Lung	lung
23	chr6:144642200-144646400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:144642200-144647600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:144642200-144647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:144642200-144654800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:144642200-144655200	Weak transcription	Thymus	Thymus
28	chr6:144642200-144659800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:144642600-144647200	Weak transcription	Fetal Heart	heart
30	chr6:144642600-144648000	Weak transcription	Fetal Lung	lung
31	chr6:144642600-144649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:144643000-144646600	Enhancers	Stomach Mucosa	stomach
33	chr6:144643200-144651600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:144643600-144648000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:144643600-144648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:144643600-144648000	Weak transcription	Gastric	stomach
37	chr6:144643600-144648000	Weak transcription	NHLF	lung
38	chr6:144643600-144648200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:144643600-144651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:144643600-144652600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:144643600-144656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:144643800-144647800	Weak transcription	Ovary	ovary
43	chr6:144643800-144648000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:144643800-144648000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:144643800-144652000	Weak transcription	HSMM	muscle
46	chr6:144643800-144663000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:144644000-144648400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:144644400-144647800	Weak transcription	HSMMtube	muscle
49	chr6:144644400-144648200	Weak transcription	Osteobl	bone
50	chr6:144644400-144652600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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