Variant report

Variant	rs209127
Chromosome Location	chr6:28870391-28870392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28870283..28872196-chr6:28873022..28875322,2	MCF-7	breast:
2	chr6:28864301..28866368-chr6:28868615..28871071,3	MCF-7	breast:
3	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
4	chr6:28805165..28806763-chr6:28869531..28871691,2	K562	blood:
5	chr6:28862622..28869079-chr6:28869294..28875315,10	MCF-7	breast:
6	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:
7	chr6:28869658..28871297-chr6:28885676..28887250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1061625	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs172326	0.90[ASN][1000 genomes]
rs1794588	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs184094	0.84[ASN][1000 genomes]
rs209140	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209147	0.88[ASN][1000 genomes]
rs209151	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209165	0.86[ASN][1000 genomes]
rs209172	0.84[ASN][1000 genomes]
rs209177	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs209180	0.82[ASN][1000 genomes]
rs2097424	0.92[ASN][1000 genomes]
rs2148007	0.84[ASN][1000 genomes]
rs2269553	0.86[ASN][1000 genomes]
rs2894066	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3130843	0.88[ASN][1000 genomes]
rs3131067	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3132377	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132380	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135314	0.83[ASN][1000 genomes]
rs393309	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs413972	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs422331	0.84[ASN][1000 genomes]
rs429369	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4484511	0.83[ASN][1000 genomes]
rs6906953	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6912843	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926892	0.81[ASN][1000 genomes]
rs743847	0.82[ASN][1000 genomes]
rs7740125	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7750338	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7769221	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs876737	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9257280	0.83[ASN][1000 genomes]
rs9257281	0.82[ASN][1000 genomes]
rs9257328	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257395	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257399	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9257412	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9257416	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257425	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs929042	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28865000-28870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28865000-28870600	Weak transcription	Stomach Mucosa	stomach
3	chr6:28865000-28870800	Weak transcription	Small Intestine	intestine
4	chr6:28865200-28870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:28865200-28871400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:28865200-28878200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:28865400-28870600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:28865400-28870600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:28865600-28870400	Weak transcription	Brain Substantia Nigra	brain
10	chr6:28865600-28870800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:28865600-28871600	Weak transcription	Fetal Heart	heart
12	chr6:28866000-28870400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:28866000-28870400	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:28866000-28870600	Weak transcription	Right Ventricle	heart
15	chr6:28866000-28870800	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:28866000-28871600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:28866000-28887000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:28866200-28870600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:28866200-28874200	Weak transcription	Right Atrium	heart
20	chr6:28866400-28870800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:28867000-28889400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:28867600-28889200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:28867600-28889400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:28867600-28889600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:28867800-28873200	Strong transcription	A549	lung
26	chr6:28867800-28874200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:28867800-28874600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:28867800-28874600	Strong transcription	NH-A	brain
29	chr6:28867800-28874600	Strong transcription	Osteobl	bone
30	chr6:28867800-28878800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:28867800-28880000	Strong transcription	Primary T cells from cord blood	blood
32	chr6:28867800-28881600	Strong transcription	HSMM	muscle
33	chr6:28867800-28883200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr6:28867800-28885400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:28867800-28888200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:28867800-28888400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:28867800-28888400	Strong transcription	Fetal Thymus	thymus
38	chr6:28867800-28889200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:28867800-28889200	Strong transcription	HMEC	breast
40	chr6:28867800-28889400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:28867800-28889400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:28867800-28889600	Strong transcription	Fetal Lung	lung
43	chr6:28868000-28878400	Strong transcription	Placenta	Placenta
44	chr6:28868000-28889200	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:28868200-28870400	Genic enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:28868200-28880200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr6:28868200-28887200	Strong transcription	HUVEC	blood vessel
48	chr6:28868200-28889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:28868200-28889800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:28868400-28872400	Strong transcription	Aorta	Aorta

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