Variant report

Variant	rs7599222
Chromosome Location	chr2:190073658-190073659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190071758..190073666-chr2:190084082..190085954,2	K562	blood:
2	chr2:190068274..190071014-chr2:190073430..190076156,3	K562	blood:
3	chr2:190070733..190073689-chr2:190074738..190076938,2	MCF-7	breast:
4	chr2:190064765..190067723-chr2:190072988..190074631,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10165127	0.85[EUR][1000 genomes]
rs10165257	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1016622	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10166385	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10167242	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10172607	0.97[ASN][1000 genomes]
rs10173224	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10184895	0.97[ASN][1000 genomes]
rs10755002	0.96[ASN][1000 genomes]
rs10931401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10931403	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10931405	0.91[ASN][1000 genomes]
rs10931411	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11901914	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12474942	0.95[ASN][1000 genomes]
rs12618316	0.88[EUR][1000 genomes]
rs12621657	0.88[ASN][1000 genomes]
rs12999125	0.93[ASN][1000 genomes]
rs13005714	1.00[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs13005834	0.88[EUR][1000 genomes]
rs13006065	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13013089	0.88[EUR][1000 genomes]
rs13015183	0.95[ASN][1000 genomes]
rs13018252	1.00[CHD][hapmap];0.94[JPT][hapmap]
rs13020999	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13024858	1.00[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs13028226	0.92[ASN][1000 genomes]
rs13030984	1.00[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs13031211	0.80[JPT][hapmap]
rs13031609	0.85[ASN][1000 genomes]
rs13035381	0.81[EUR][1000 genomes]
rs13408928	0.99[ASN][1000 genomes]
rs13411992	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13413518	0.99[ASN][1000 genomes]
rs1356161	0.94[ASN][1000 genomes]
rs1356166	0.92[ASN][1000 genomes]
rs1464135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474000	0.90[ASN][1000 genomes]
rs1515864	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1515866	0.96[ASN][1000 genomes]
rs1515869	0.85[EUR][1000 genomes]
rs1520858	0.89[CEU][hapmap];0.94[JPT][hapmap]
rs1533618	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546617	0.94[ASN][1000 genomes]
rs1913892	0.94[ASN][1000 genomes]
rs1949327	1.00[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1973666	0.89[ASN][1000 genomes]
rs1983318	0.92[ASN][1000 genomes]
rs2138373	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2351631	0.96[ASN][1000 genomes]
rs2351632	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2351633	0.95[ASN][1000 genomes]
rs2351635	0.87[ASN][1000 genomes]
rs36019389	0.86[EUR][1000 genomes]
rs4128538	0.88[CHD][hapmap]
rs4417749	1.00[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs4667263	0.85[EUR][1000 genomes]
rs4667266	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4667268	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4667270	0.99[ASN][1000 genomes]
rs4667271	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4667275	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6434324	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6434325	0.85[EUR][1000 genomes]
rs6434334	0.92[ASN][1000 genomes]
rs6434337	0.89[ASN][1000 genomes]
rs6704568	0.89[ASN][1000 genomes]
rs6728877	0.92[ASN][1000 genomes]
rs6732534	0.95[ASN][1000 genomes]
rs6741804	0.85[EUR][1000 genomes]
rs6749559	1.00[CEU][hapmap]
rs6752781	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6761868	0.89[ASN][1000 genomes]
rs7556928	0.81[EUR][1000 genomes]
rs7560973	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7574281	0.90[ASN][1000 genomes]
rs7593860	0.85[EUR][1000 genomes]
rs7603704	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7606337	0.85[EUR][1000 genomes]
rs9288163	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs939158	0.87[ASN][1000 genomes]
rs939160	0.96[ASN][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7599222	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190069800-190074400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:190070000-190074600	Weak transcription	HMEC	breast
3	chr2:190070200-190074000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:190070200-190074200	Weak transcription	NHEK	skin
5	chr2:190070400-190074400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:190071200-190075000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:190072200-190074800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:190072600-190074800	Enhancers	Adipose Nuclei	Adipose
9	chr2:190072600-190076000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:190072800-190073800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:190072800-190074600	Enhancers	NHDF-Ad	bronchial
12	chr2:190072800-190074600	Enhancers	Osteobl	bone
13	chr2:190072800-190074800	Enhancers	HUVEC	blood vessel
14	chr2:190072800-190074800	Enhancers	NHLF	lung
15	chr2:190072800-190075000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:190072800-190075800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:190073000-190073800	Enhancers	K562	blood
18	chr2:190073000-190074400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:190073000-190074600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:190073000-190075400	Enhancers	Hela-S3	cervix
21	chr2:190073000-190077000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:190073000-190077000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr2:190073200-190073800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:190073200-190073800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:190073200-190073800	Enhancers	Ovary	ovary
26	chr2:190073200-190074600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:190073200-190074800	Enhancers	NH-A	brain
28	chr2:190073200-190075400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr2:190073200-190075400	Enhancers	Fetal Stomach	stomach
30	chr2:190073200-190075400	Enhancers	HSMM	muscle
31	chr2:190073200-190075800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr2:190073200-190077000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:190073400-190073800	Flanking Active TSS	A549	lung
34	chr2:190073400-190074000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:190073400-190074400	Weak transcription	Fetal Lung	lung
36	chr2:190073400-190074800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:190073400-190074800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:190073400-190077000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr2:190073600-190073800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:190073600-190073800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:190073600-190073800	Enhancers	Aorta	Aorta
42	chr2:190073600-190074600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:190073600-190075400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:190073600-190076600	Weak transcription	H9 Cell Line	embryonic stem cell

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