Variant report

Variant	rs2144328
Chromosome Location	chr6:38565391-38565392
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	chr6:38565254..38567561-chr6:38606168..38608897,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183826	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10807196	0.85[CEU][hapmap]
rs10807198	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947752	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1321056	0.89[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699001	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1699002	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1699003	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699004	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1699005	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1699007	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699017	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1739621	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1739626	0.89[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1739627	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1739628	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1739629	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1739630	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1739632	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1739633	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1781708	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1781711	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1781712	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1852979	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2252550	0.85[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2748172	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2814883	0.81[CEU][hapmap]
rs2814889	0.81[CEU][hapmap]
rs2814894	0.89[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4392718	0.85[CEU][hapmap]
rs6458059	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910516	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394521	0.87[EUR][1000 genomes];0.83[ASN][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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
2	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:38536800-38566400	Weak transcription	Pancreas	Pancrea
4	chr6:38538000-38566800	Weak transcription	Esophagus	oesophagus
5	chr6:38540400-38567800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:38540400-38569200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:38541400-38568600	Weak transcription	Spleen	Spleen
8	chr6:38541600-38567000	Weak transcription	Small Intestine	intestine
9	chr6:38545400-38566000	Weak transcription	Colonic Mucosa	Colon
10	chr6:38547400-38565400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:38547400-38566600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:38548200-38570800	Weak transcription	Fetal Kidney	kidney
13	chr6:38549000-38570800	Weak transcription	Fetal Intestine Small	intestine
14	chr6:38555000-38565800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:38556000-38580400	Weak transcription	Ovary	ovary
16	chr6:38556200-38567400	Weak transcription	Lung	lung
17	chr6:38557400-38571800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:38557400-38571800	Weak transcription	NHDF-Ad	bronchial
19	chr6:38557400-38578000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:38557800-38571600	Weak transcription	HMEC	breast
21	chr6:38557800-38572000	Weak transcription	NHLF	lung
22	chr6:38558400-38566000	Strong transcription	Primary B cells from cord blood	blood
23	chr6:38558600-38565800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:38558800-38567400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:38559600-38565400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:38559600-38567400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:38560600-38566800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:38560600-38567400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:38560600-38568200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:38560600-38570800	Weak transcription	Fetal Intestine Large	intestine
31	chr6:38560600-38570800	Weak transcription	Left Ventricle	heart
32	chr6:38560600-38570800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:38560600-38571000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:38560600-38571800	Weak transcription	HSMM	muscle
35	chr6:38560600-38574400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:38560800-38570800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:38560800-38571400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:38560800-38580000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:38560800-38580200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:38561400-38577600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:38561400-38578000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:38561600-38571400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:38561800-38571600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:38561800-38571600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:38562000-38565400	Weak transcription	Placenta	Placenta
46	chr6:38562000-38567600	Weak transcription	Brain Anterior Caudate	brain
47	chr6:38562000-38570600	Weak transcription	Fetal Lung	lung
48	chr6:38562000-38570800	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:38562000-38571800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:38562000-38574600	Weak transcription	Fetal Muscle Leg	muscle

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