Variant report

Variant	rs3788420
Chromosome Location	chr22:30376919-30376920
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30369409..30372830-chr22:30374993..30377919,3	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1076135	0.82[CEU][hapmap]
rs12710565	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs140145	0.85[CEU][hapmap]
rs140147	0.92[CEU][hapmap]
rs140149	0.85[CEU][hapmap]
rs1548389	0.89[CEU][hapmap]
rs1807508	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1807513	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1989870	0.92[CEU][hapmap]
rs2007446	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2007458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189802	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2285667	0.90[EUR][1000 genomes]
rs3747149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747150	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41155	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41156	0.83[EUR][1000 genomes]
rs41157	0.83[EUR][1000 genomes]
rs41158	0.86[ASN][1000 genomes]
rs41159	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41161	0.86[EUR][1000 genomes]
rs41165	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41168	0.92[CEU][hapmap]
rs41171	0.93[CEU][hapmap]
rs41173	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs4630869	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820824	1.00[ASN][1000 genomes]
rs55805200	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752964	0.81[CEU][hapmap]
rs5752973	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5752975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5752978	0.96[CEU][hapmap]
rs5752992	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763559	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763565	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5763581	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5763589	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763591	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763614	0.84[EUR][1000 genomes]
rs5763638	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763645	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763646	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763649	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763650	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763651	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763670	0.89[EUR][1000 genomes]
rs5763671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763688	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763775	0.89[CEU][hapmap]
rs5763779	0.92[CEU][hapmap]
rs59663694	0.89[EUR][1000 genomes]
rs5997546	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6006300	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7285583	0.81[EUR][1000 genomes]
rs7289604	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73162764	0.88[EUR][1000 genomes]
rs737908	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737911	0.89[CEU][hapmap]
rs737939	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9306468	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs960987	0.85[EUR][1000 genomes]
rs997913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv3591	chr22:30344208-30388897	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 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	chr22:30345400-30379000	Weak transcription	Esophagus	oesophagus
2	chr22:30348400-30387200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
4	chr22:30351200-30385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr22:30351200-30387400	Weak transcription	Ovary	ovary
6	chr22:30352800-30388600	Weak transcription	HepG2	liver
7	chr22:30354600-30390200	Weak transcription	Colonic Mucosa	Colon
8	chr22:30354800-30390400	Weak transcription	Small Intestine	intestine
9	chr22:30358800-30387400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr22:30366000-30384200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr22:30366400-30387400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr22:30366600-30390800	Weak transcription	Gastric	stomach
14	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr22:30368400-30382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr22:30368400-30387400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr22:30369400-30382600	Weak transcription	Brain Anterior Caudate	brain
19	chr22:30369400-30388400	Weak transcription	NH-A	brain
20	chr22:30370000-30391000	Weak transcription	Fetal Heart	heart
21	chr22:30370200-30388400	Weak transcription	NHLF	lung
22	chr22:30370600-30390800	Weak transcription	Right Ventricle	heart
23	chr22:30370800-30379400	Weak transcription	HSMM	muscle
24	chr22:30370800-30387400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr22:30370800-30390000	Weak transcription	Stomach Mucosa	stomach
26	chr22:30371000-30383200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr22:30371200-30382000	Weak transcription	Brain Substantia Nigra	brain
28	chr22:30371800-30385800	Weak transcription	Lung	lung
29	chr22:30371800-30386600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr22:30372600-30377800	Strong transcription	Fetal Muscle Leg	muscle
31	chr22:30373400-30383000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr22:30373400-30388600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr22:30373600-30377600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr22:30373600-30377800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr22:30373600-30383400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr22:30373600-30383600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr22:30373600-30388600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr22:30373800-30377600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr22:30373800-30391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr22:30374000-30377400	Strong transcription	Placenta	Placenta
41	chr22:30374000-30377600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr22:30374000-30380000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr22:30374200-30377000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr22:30374200-30377000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr22:30374200-30377200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr22:30374200-30377400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr22:30374200-30377600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr22:30374200-30389600	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr22:30374400-30377400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr22:30374400-30377600	Strong transcription	Fetal Muscle Trunk	muscle

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