Variant report

Variant	rs2228210
Chromosome Location	chr6:12122174-12122175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:12121380-12123213	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:12121895-12123049	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:12121188-12122320	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:12121882-12122196	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:12121158-12122273	K562	blood:	n/a	n/a
6	POLR2A	chr6:12120206-12127200	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

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	chr6:12112214..12113885-chr6:12120290..12122311,2	MCF-7	breast:
4	chr6:12121354..12124160-chr6:12124387..12127590,3	K562	blood:
5	chr6:12110770..12113463-chr6:12121895..12124964,3	K562	blood:

No data

Variant related genes	Relation type
HIVEP1	TF binding region
ENSG00000095951	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10947758	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947793	0.87[AMR][1000 genomes];0.88[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[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13193986	0.97[AMR][1000 genomes];0.94[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];1.00[YRI][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];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228209	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[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2327514	1.00[LWK][hapmap]
rs3777755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[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];0.93[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];0.94[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];0.98[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];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4377779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4467770	0.94[CHB][hapmap];0.80[CHD][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];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6939913	0.88[CEU][hapmap];0.94[CHB][hapmap];0.80[CHD][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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7752678	0.95[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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366985	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369076	0.88[CEU][hapmap];0.94[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9369083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369108	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][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[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380859	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9394538	0.97[AMR][1000 genomes];0.95[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	chr6:12107400-12124800	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:12116000-12128000	Weak transcription	Fetal Heart	heart
4	chr6:12117200-12136800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:12118400-12138400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:12118800-12131400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:12119200-12123000	Strong transcription	Primary hematopoietic stem cells	blood
8	chr6:12119200-12125000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:12119400-12126000	Strong transcription	Fetal Muscle Leg	muscle
10	chr6:12119400-12126200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:12119400-12129800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:12119600-12122800	Weak transcription	Stomach Mucosa	stomach
13	chr6:12119600-12126800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:12119800-12122200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:12119800-12122800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:12119800-12138800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:12120000-12128800	Strong transcription	Liver	Liver
18	chr6:12120200-12122200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:12120200-12122200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr6:12120200-12122200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr6:12120200-12122200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:12120200-12122400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:12120200-12122400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:12120200-12122400	Strong transcription	Lung	lung
25	chr6:12120200-12122400	ZNF genes & repeats	GM12878-XiMat	blood
26	chr6:12120200-12122600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:12120200-12122800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:12120200-12122800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:12120200-12122800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr6:12120200-12122800	Strong transcription	Right Ventricle	heart
31	chr6:12120200-12122800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:12120200-12122800	ZNF genes & repeats	K562	blood
33	chr6:12120200-12123400	Strong transcription	NH-A	brain
34	chr6:12120200-12123600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:12120200-12123600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:12120200-12123800	Strong transcription	Primary T cells from cord blood	blood
37	chr6:12120200-12124800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:12120200-12124800	Strong transcription	Fetal Thymus	thymus
39	chr6:12120200-12124800	Strong transcription	Thymus	Thymus
40	chr6:12120200-12125000	Strong transcription	Fetal Intestine Large	intestine
41	chr6:12120200-12125200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:12120200-12126000	Strong transcription	Left Ventricle	heart
43	chr6:12120200-12126000	Strong transcription	HUVEC	blood vessel
44	chr6:12120200-12129000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:12120400-12122200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:12120400-12122200	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:12120400-12122200	Strong transcription	Brain Hippocampus Middle	brain
48	chr6:12120400-12122200	Strong transcription	Colonic Mucosa	Colon
49	chr6:12120400-12122200	Strong transcription	Ovary	ovary
50	chr6:12120400-12122200	Strong transcription	Placenta Amnion	Placenta Amnion

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