Variant report

Variant	rs2228209
Chromosome Location	chr6:12120588-12120589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12012948..12015001-chr6:12120385..12122503,2	K562	blood:
2	chr6:12120255..12124315-chr6:12124957..12127895,3	MCF-7	breast:
3	chr6:12119694..12121745-chr6:12128409..12130383,2	MCF-7	breast:
4	chr6:12101827..12103669-chr6:12119606..12121649,2	K562	blood:
5	chr6:12112214..12113885-chr6:12120290..12122311,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095951	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10947758	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947793	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12199075	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12210300	0.83[JPT][hapmap]
rs12213070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13193986	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13206426	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13209918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4377779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4467770	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs4714201	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4714232	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6939913	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7383768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7752678	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296258	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9357299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366985	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369076	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9369083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369108	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380859	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9394538	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv870443	chr6:12096356-12125998	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12091000-12130600	Weak transcription	Psoas Muscle	Psoas
2	chr6:12106000-12120600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:12106000-12120600	Weak transcription	Esophagus	oesophagus
4	chr6:12107400-12124800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:12107600-12120800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:12107800-12120600	Weak transcription	Brain Angular Gyrus	brain
7	chr6:12113400-12120600	Weak transcription	Placenta	Placenta
8	chr6:12113800-12121400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:12114200-12120800	Weak transcription	NHDF-Ad	bronchial
10	chr6:12114200-12121000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:12114400-12120800	Weak transcription	Osteobl	bone
12	chr6:12116000-12128000	Weak transcription	Fetal Heart	heart
13	chr6:12117000-12120600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:12117000-12120600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:12117200-12120600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:12117200-12136800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:12117400-12121000	Weak transcription	Brain Substantia Nigra	brain
18	chr6:12117800-12120600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:12118200-12120600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:12118200-12120600	Weak transcription	Brain Germinal Matrix	brain
21	chr6:12118400-12120600	Weak transcription	Brain Anterior Caudate	brain
22	chr6:12118400-12120600	Weak transcription	Fetal Brain Female	brain
23	chr6:12118400-12138400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:12118800-12131400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:12119200-12123000	Strong transcription	Primary hematopoietic stem cells	blood
26	chr6:12119200-12125000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:12119400-12121200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:12119400-12121600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:12119400-12126000	Strong transcription	Fetal Muscle Leg	muscle
30	chr6:12119400-12126200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:12119400-12129800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:12119600-12120600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:12119600-12121000	Weak transcription	Fetal Intestine Small	intestine
34	chr6:12119600-12122800	Weak transcription	Stomach Mucosa	stomach
35	chr6:12119600-12126800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:12119800-12120600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:12119800-12122200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:12119800-12122800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:12119800-12138800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr6:12120000-12120600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:12120000-12120600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:12120000-12120600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:12120000-12128800	Strong transcription	Liver	Liver
44	chr6:12120200-12120600	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr6:12120200-12122000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:12120200-12122200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:12120200-12122200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr6:12120200-12122200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr6:12120200-12122200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr6:12120200-12122400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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