Variant report

Variant	rs2071578
Chromosome Location	chr22:29725893-29725894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29723486..29726017-chr22:29727288..29729137,2	MCF-7	breast:
2	chr22:29701505..29704721-chr22:29721557..29726932,5	MCF-7	breast:
3	chr22:29714571..29716795-chr22:29725511..29728000,2	K562	blood:
4	chr22:29714617..29716515-chr22:29723959..29726093,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185340	Chromatin interaction
ENSG00000100276	Chromatin interaction
ENSG00000100280	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11090564	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs131180	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131182	0.87[ASN][1000 genomes]
rs131189	0.87[ASN][1000 genomes]
rs140062	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs140063	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs140066	0.91[ASN][1000 genomes]
rs174759	0.94[ASN][1000 genomes]
rs174761	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs174762	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs174764	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174765	0.94[ASN][1000 genomes]
rs174766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174767	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs174769	0.91[ASN][1000 genomes]
rs174770	0.94[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs174771	0.91[ASN][1000 genomes]
rs174775	0.83[CHD][hapmap]
rs2072051	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs2267132	0.81[CHB][hapmap]
rs2267133	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs2283849	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283850	0.94[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2301290	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs2301585	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2519486	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2857462	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2857466	0.83[JPT][hapmap]
rs28755	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3788410	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3788411	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4820803	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4820804	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752903	0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.91[ASN][1000 genomes]
rs5763138	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs5763139	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763178	0.91[ASN][1000 genomes]
rs6006090	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6006098	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs715494	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs879580	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs9537	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs98069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29707400-29740000	Weak transcription	Hela-S3	cervix
2	chr22:29711800-29733400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr22:29719400-29730600	Weak transcription	HepG2	liver
4	chr22:29719600-29730800	Weak transcription	HMEC	breast
5	chr22:29720200-29726800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr22:29720600-29726000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:29720600-29732200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:29720600-29740000	Weak transcription	Fetal Brain Male	brain
9	chr22:29721200-29726800	Weak transcription	Right Atrium	heart
10	chr22:29721200-29732000	Weak transcription	K562	blood
11	chr22:29721400-29727000	Strong transcription	Placenta	Placenta
12	chr22:29721400-29738200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr22:29721400-29746800	Strong transcription	Fetal Intestine Small	intestine
14	chr22:29721800-29726000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr22:29721800-29728200	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr22:29721800-29734400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr22:29721800-29739600	Strong transcription	Colonic Mucosa	Colon
18	chr22:29721800-29756800	Strong transcription	Primary T cells from cord blood	blood
19	chr22:29722000-29726400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr22:29722000-29727200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr22:29722000-29732400	Strong transcription	Gastric	stomach
22	chr22:29722000-29732800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr22:29722000-29739200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr22:29722000-29739800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr22:29722000-29747000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr22:29722000-29759200	Strong transcription	Dnd41	blood
27	chr22:29722000-29759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr22:29722200-29726600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr22:29722200-29726600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr22:29722200-29726800	Strong transcription	Adipose Nuclei	Adipose
31	chr22:29722200-29726800	Strong transcription	Fetal Intestine Large	intestine
32	chr22:29722200-29726800	Strong transcription	Right Ventricle	heart
33	chr22:29722200-29726800	Strong transcription	NHLF	lung
34	chr22:29722200-29727000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr22:29722200-29727000	Strong transcription	Lung	lung
36	chr22:29722200-29727000	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr22:29722200-29727200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr22:29722200-29730000	Strong transcription	Liver	Liver
39	chr22:29722200-29733000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr22:29722200-29737000	Strong transcription	Pancreas	Pancrea
41	chr22:29722200-29738000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr22:29722200-29738000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr22:29722200-29739400	Strong transcription	Fetal Brain Female	brain
44	chr22:29722200-29741000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr22:29722200-29755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr22:29722200-29756400	Strong transcription	Thymus	Thymus
47	chr22:29722200-29756600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr22:29722200-29759800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr22:29722400-29726200	Strong transcription	Esophagus	oesophagus
50	chr22:29722400-29726800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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