Variant report

Variant	rs9474639
Chromosome Location	chr6:53593172-53593173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53375847..53377727-chr6:53591880..53594689,2	MCF-7	breast:
2	chr6:53593116..53596418-chr6:53657644..53660881,3	MCF-7	breast:
3	chr6:53357447..53358709-chr6:53592427..53594072,11	K562	blood:
4	chr6:53590810..53593190-chr6:53597036..53600341,4	K562	blood:
5	chr6:53357659..53358540-chr6:53592973..53593762,2	MCF-7	breast:
6	chr6:53589302..53590903-chr6:53592714..53595336,2	K562	blood:
7	chr6:53592971..53596675-chr6:53657710..53661284,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10456672	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11751003	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11758147	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13216331	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4345397	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4373352	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4400206	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4404762	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4441952	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4457161	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4516937	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4563705	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4610551	0.80[AMR][1000 genomes]
rs4712043	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4712044	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4715418	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6908232	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6921605	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs6925356	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6934324	0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7749273	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7756512	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7763482	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7773852	0.85[CHB][hapmap]
rs7776124	0.90[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382235	0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes]
rs9474640	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9474641	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9474646	0.90[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9474649	0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53588800-53594600	Enhancers	Placenta	Placenta
2	chr6:53589400-53594400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:53589600-53593200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:53589600-53593600	Enhancers	HepG2	liver
5	chr6:53589800-53594800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:53589800-53595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:53589800-53595000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:53589800-53599400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:53590000-53593200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:53590000-53593200	Weak transcription	Fetal Intestine Large	intestine
11	chr6:53590000-53593200	Weak transcription	Fetal Intestine Small	intestine
12	chr6:53590000-53595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:53590200-53595000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:53590800-53593200	Weak transcription	Fetal Kidney	kidney
15	chr6:53591000-53593200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:53591000-53593200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:53591000-53593200	Weak transcription	Adipose Nuclei	Adipose
18	chr6:53591000-53593200	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:53591000-53596800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:53591000-53599000	Weak transcription	Stomach Mucosa	stomach
21	chr6:53591200-53593200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:53591200-53593200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:53591200-53593200	Weak transcription	Liver	Liver
24	chr6:53591200-53593200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:53591200-53593200	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:53591200-53593200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:53591200-53593400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:53591200-53593400	Weak transcription	Left Ventricle	heart
29	chr6:53591200-53595000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:53591200-53596600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:53591200-53599600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:53591200-53599800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:53591600-53599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:53592200-53593200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:53592200-53593600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:53592400-53593200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:53592400-53593200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:53592400-53593200	Enhancers	Hela-S3	cervix
39	chr6:53592400-53593600	Enhancers	HSMM	muscle
40	chr6:53592400-53593600	Enhancers	HSMMtube	muscle
41	chr6:53592400-53593600	Enhancers	NH-A	brain
42	chr6:53592400-53593800	Enhancers	A549	lung
43	chr6:53592400-53593800	Enhancers	HMEC	breast
44	chr6:53592600-53593200	Enhancers	Osteobl	bone
45	chr6:53592600-53593600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:53592600-53593600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:53592600-53593800	Enhancers	Placenta Amnion	Placenta Amnion
48	chr6:53592600-53593800	Enhancers	NHEK	skin
49	chr6:53592800-53593600	Active TSS	NHDF-Ad	bronchial
50	chr6:53592800-53596600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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