Variant report

Variant	rs28257
Chromosome Location	chr22:30429115-30429116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99426397..99429195-chr22:30427299..30429997,2	MCF-7	breast:
2	chr22:30426124..30429580-chr22:30433201..30436027,3	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1071888	0.80[EUR][1000 genomes]
rs11090598	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12167333	0.84[EUR][1000 genomes]
rs12168499	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12168552	0.82[EUR][1000 genomes]
rs12171061	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12171250	0.86[EUR][1000 genomes]
rs12171263	0.82[EUR][1000 genomes]
rs17643918	0.83[EUR][1000 genomes]
rs17648725	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1807509	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs193473	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs193481	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1978083	0.82[EUR][1000 genomes]
rs2017677	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2051764	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2412960	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2412963	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34862234	0.83[EUR][1000 genomes]
rs35705048	0.82[EUR][1000 genomes]
rs36580	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36590	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36591	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36594	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36596	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36598	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36600	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36601	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36604	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36605	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36606	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36607	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3788423	0.95[CEU][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3887275	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3958025	0.87[CEU][hapmap]
rs39712	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41162	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41164	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs41166	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41172	0.87[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs41174	0.87[CEU][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs41175	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41177	0.80[CEU][hapmap]
rs41178	1.00[ASN][1000 genomes]
rs41179	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239932	0.95[CEU][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4239933	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4337577	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4823063	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4823070	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4993442	0.81[EUR][1000 genomes]
rs5752968	0.86[CEU][hapmap]
rs5752986	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5752988	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5752993	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763630	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763634	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763644	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763674	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763675	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5763680	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5763689	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5763691	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs715523	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs718772	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7286070	0.83[EUR][1000 genomes]
rs7292615	0.83[EUR][1000 genomes]
rs737904	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs737909	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs737912	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs7510705	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8135823	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8136147	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8138286	0.82[EUR][1000 genomes]
rs8139994	0.82[EUR][1000 genomes]
rs8141404	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8141680	0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8141765	0.82[EUR][1000 genomes]
rs9620926	0.83[EUR][1000 genomes]
rs9620943	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9620953	0.85[EUR][1000 genomes]
rs9625873	0.84[EUR][1000 genomes]
rs9625874	0.84[EUR][1000 genomes]
rs9625878	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9625879	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9625919	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9625926	0.87[EUR][1000 genomes]
rs9625931	0.84[EUR][1000 genomes]
rs9625933	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr22:30409000-30432800	Strong transcription	Fetal Stomach	stomach
4	chr22:30412000-30431200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:30419600-30434400	Weak transcription	Small Intestine	intestine
6	chr22:30422400-30434200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr22:30422400-30434200	Weak transcription	HUVEC	blood vessel
8	chr22:30422800-30429600	Weak transcription	NHDF-Ad	bronchial
9	chr22:30422800-30429800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr22:30423000-30429600	Weak transcription	Fetal Heart	heart
11	chr22:30423000-30432600	Weak transcription	NH-A	brain
12	chr22:30423400-30429400	Weak transcription	Colon Smooth Muscle	Colon
13	chr22:30423400-30429600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr22:30423400-30429600	Weak transcription	GM12878-XiMat	blood
15	chr22:30423400-30430800	Strong transcription	Fetal Intestine Small	intestine
16	chr22:30423400-30432400	Weak transcription	Stomach Mucosa	stomach
17	chr22:30423400-30434400	Weak transcription	A549	lung
18	chr22:30423600-30447600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr22:30424200-30429600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:30424200-30429800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr22:30424200-30434000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr22:30424400-30429400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr22:30424400-30429800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:30424400-30431400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr22:30424600-30429600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr22:30424600-30429800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr22:30424600-30432600	Weak transcription	HMEC	breast
28	chr22:30424600-30435600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr22:30424800-30429600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr22:30424800-30432400	Weak transcription	Colonic Mucosa	Colon
31	chr22:30424800-30443000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:30425000-30429600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr22:30425000-30430600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr22:30425000-30434200	Weak transcription	Gastric	stomach
35	chr22:30425200-30429200	Weak transcription	Right Atrium	heart
36	chr22:30425200-30429200	Weak transcription	Right Ventricle	heart
37	chr22:30425200-30429400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:30425200-30429400	Weak transcription	Adipose Nuclei	Adipose
39	chr22:30425200-30429600	Weak transcription	Spleen	Spleen
40	chr22:30425200-30429800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr22:30425200-30430400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr22:30425200-30431600	Weak transcription	Esophagus	oesophagus
43	chr22:30425200-30432400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr22:30425200-30432400	Weak transcription	HSMMtube	muscle
45	chr22:30425200-30434000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr22:30425200-30434200	Weak transcription	Pancreas	Pancrea
47	chr22:30425200-30434200	Weak transcription	NHLF	lung
48	chr22:30425200-30435800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr22:30425200-30438800	Weak transcription	Fetal Intestine Large	intestine
50	chr22:30425200-30440000	Weak transcription	Fetal Lung	lung

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