Variant report

Variant	rs9625874
Chromosome Location	chr22:30288625-30288626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30288615..30290652-chr22:30302494..30304851,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1071888	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076137	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12168552	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171061	0.82[EUR][1000 genomes]
rs131278	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap]
rs131291	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MKK][hapmap];0.90[YRI][hapmap]
rs131294	0.80[AMR][1000 genomes]
rs131296	0.83[CHD][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs140105	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap]
rs140108	0.88[JPT][hapmap];0.82[YRI][hapmap]
rs140135	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs140151	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17643918	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807509	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs193473	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs193481	0.84[EUR][1000 genomes]
rs2017677	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051764	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2105870	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2349225	0.82[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs2412960	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412963	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249400	0.89[ASN][1000 genomes]
rs28257	0.84[EUR][1000 genomes]
rs34862234	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35705048	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36578	0.88[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs36580	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36590	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36591	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36594	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36596	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36598	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36600	0.82[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36601	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36604	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36605	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36606	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36607	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788423	0.84[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3887275	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3958025	0.82[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.85[MKK][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39712	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41162	0.86[CEU][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs41164	0.82[CEU][hapmap]
rs41166	0.80[EUR][1000 genomes]
rs41172	0.88[GIH][hapmap]
rs41175	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41179	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4239932	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820820	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4820822	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4823055	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4823063	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4993442	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752968	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752986	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752988	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5752993	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763630	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763634	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763644	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763674	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763675	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763680	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763689	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763691	0.81[EUR][1000 genomes]
rs715523	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7286070	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7292615	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737904	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs737909	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs737912	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7510705	0.82[AFR][1000 genomes]
rs8136147	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8139994	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8141404	0.86[CEU][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs8141680	1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9620926	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625873	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625878	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625879	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1851082	chr22:30253256-30294744	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1833221	chr22:30274129-30297376	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv829161	chr22:30276811-30298332	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv829162	chr22:30276811-30298761	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv11554	chr22:30280400-30298271	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv1825528	chr22:30282800-30295577	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9625874	KIAA1671	cis	cerebellum	SCAN
rs9625874	CRYBB3	cis	parietal	SCAN
rs9625874	MTMR3	cis	parietal	SCAN
rs9625874	TTC28	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30280200-30293600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:30280200-30303800	Weak transcription	Aorta	Aorta
3	chr22:30280400-30297400	Weak transcription	K562	blood
4	chr22:30280800-30291600	Weak transcription	Lung	lung
5	chr22:30280800-30303600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr22:30281000-30303000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr22:30281000-30303200	Weak transcription	Fetal Muscle Leg	muscle
8	chr22:30281400-30312200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr22:30281600-30303400	Weak transcription	Fetal Intestine Small	intestine
10	chr22:30281800-30299000	Weak transcription	Spleen	Spleen
11	chr22:30281800-30300200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr22:30282000-30297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr22:30282200-30290400	Weak transcription	Fetal Stomach	stomach
14	chr22:30282200-30303000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr22:30282200-30303200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr22:30282200-30310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr22:30282600-30290200	Weak transcription	Fetal Brain Male	brain
18	chr22:30282600-30300000	Weak transcription	Small Intestine	intestine
19	chr22:30282600-30303400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr22:30283800-30289600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr22:30283800-30290000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr22:30283800-30290200	Weak transcription	Fetal Heart	heart
23	chr22:30283800-30292600	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr22:30283800-30294200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr22:30283800-30294400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:30283800-30295600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr22:30283800-30297400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr22:30283800-30299000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr22:30283800-30300000	Weak transcription	Stomach Mucosa	stomach
30	chr22:30283800-30307000	Weak transcription	Esophagus	oesophagus
31	chr22:30284000-30288800	Weak transcription	Colon Smooth Muscle	Colon
32	chr22:30284000-30290000	Weak transcription	Brain Hippocampus Middle	brain
33	chr22:30284000-30297200	Weak transcription	Primary B cells from cord blood	blood
34	chr22:30284000-30299800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr22:30284000-30303600	Weak transcription	Brain Angular Gyrus	brain
36	chr22:30284400-30288800	Weak transcription	Liver	Liver
37	chr22:30284400-30303800	Weak transcription	Pancreas	Pancrea
38	chr22:30284600-30288800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr22:30284600-30290400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr22:30286400-30288800	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr22:30286800-30290000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr22:30287000-30290000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr22:30287000-30294600	Weak transcription	Gastric	stomach
44	chr22:30287000-30301000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr22:30287000-30319600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr22:30287600-30290000	Weak transcription	Left Ventricle	heart
47	chr22:30287600-30290200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr22:30287600-30293200	Weak transcription	Ovary	ovary
49	chr22:30287600-30294000	Weak transcription	Right Ventricle	heart
50	chr22:30287800-30288800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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