Variant report

Variant	rs6430935
Chromosome Location	chr2:128006991-128006992
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	chr2:127983318..127986030-chr2:128006327..128008431,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10209678	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10803585	0.83[ASN][1000 genomes]
rs10928761	0.89[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10928764	0.86[CEU][hapmap]
rs1143407	0.86[CEU][hapmap];0.91[MEX][hapmap]
rs11684068	0.89[CEU][hapmap]
rs11886231	0.96[ASN][1000 genomes]
rs11890187	0.88[ASN][1000 genomes]
rs12052483	0.82[ASN][1000 genomes]
rs12463451	0.91[ASN][1000 genomes]
rs12465955	0.99[ASN][1000 genomes]
rs12477214	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12479003	0.84[ASN][1000 genomes]
rs12613413	0.86[CEU][hapmap];0.83[MEX][hapmap]
rs12622436	0.86[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs12623948	0.96[ASN][1000 genomes]
rs12692064	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12989081	0.83[ASN][1000 genomes]
rs12989154	0.84[ASN][1000 genomes]
rs13029237	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs13429925	0.86[CEU][hapmap];0.83[MEX][hapmap]
rs1566823	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs17015199	0.88[ASN][1000 genomes]
rs1850689	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2090574	0.83[ASN][1000 genomes]
rs2134794	0.86[CEU][hapmap];0.91[MEX][hapmap]
rs2174270	0.99[ASN][1000 genomes]
rs2276583	0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2276682	0.86[CEU][hapmap]
rs2896980	0.82[ASN][1000 genomes]
rs34703177	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs34832797	0.84[ASN][1000 genomes]
rs35293119	0.82[ASN][1000 genomes]
rs35328149	0.96[ASN][1000 genomes]
rs3738948	0.86[CEU][hapmap]
rs3768866	0.96[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4150407	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4150434	0.86[CEU][hapmap]
rs4150441	0.96[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs4150454	0.96[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs4150477	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs4150495	0.96[ASN][1000 genomes]
rs4150496	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs4150506	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs4233583	0.96[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs4233584	0.91[ASN][1000 genomes]
rs4497825	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs4662575	0.97[ASN][1000 genomes]
rs4662578	0.88[ASN][1000 genomes]
rs4662580	0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[ASN][1000 genomes]
rs4662711	0.93[ASN][1000 genomes]
rs4662712	0.84[ASN][1000 genomes]
rs4662717	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs4662721	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs4662722	0.87[ASN][1000 genomes]
rs4662724	0.86[CEU][hapmap];0.83[MEX][hapmap]
rs4662725	0.82[ASN][1000 genomes]
rs55905117	0.98[ASN][1000 genomes]
rs55998967	0.93[ASN][1000 genomes]
rs58475809	0.96[ASN][1000 genomes]
rs59566504	0.85[ASN][1000 genomes]
rs62157549	0.88[ASN][1000 genomes]
rs62157555	0.87[ASN][1000 genomes]
rs6430937	0.85[CEU][hapmap];0.83[MEX][hapmap]
rs6712213	0.96[ASN][1000 genomes]
rs6712446	0.96[ASN][1000 genomes]
rs6712551	0.96[ASN][1000 genomes]
rs6716392	0.81[CEU][hapmap]
rs6731176	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs6732279	0.96[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs6735779	0.84[CEU][hapmap]
rs6747862	0.81[CEU][hapmap]
rs6761447	0.88[ASN][1000 genomes]
rs71414745	0.91[ASN][1000 genomes]
rs7568261	0.84[ASN][1000 genomes]
rs7580658	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs7589451	0.83[ASN][1000 genomes]
rs867304	0.88[ASN][1000 genomes]
rs9636237	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs9789510	0.96[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6430935	AC068282.3	cis	Muscle Skeletal	GTEx
rs6430935	AC068282.3	cis	Stomach	GTEx
rs6430935	MAP3K2	cis	Cerebellum	GTEx
rs6430935	AC068282.3	cis	Esophagus Muscularis	GTEx
rs6430935	MAP3K2	cis	multi-tissue	Pritchard
rs6430935	AC068282.3	cis	Heart Left Ventricle	GTEx
rs6430935	AC068282.3	cis	Artery Aorta	GTEx
rs6430935	AC068282.3	cis	Whole Blood	GTEx
rs6430935	AC068282.3	cis	Thyroid	GTEx
rs6430935	AC068282.3	cis	lung	GTEx
rs6430935	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6430935	MAP3K2	cis	Frontal Cortex	GTEx
rs6430935	AC068282.3	cis	Artery Tibial	GTEx
rs6430935	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs6430935	AC068282.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127984600-128012800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:127989400-128013000	Weak transcription	Pancreas	Pancrea
3	chr2:127996400-128013400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:127996400-128013400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:127999200-128012200	Weak transcription	Liver	Liver
6	chr2:128000000-128013400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:128000400-128013400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:128001400-128012000	Weak transcription	A549	lung
9	chr2:128002400-128015800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:128002800-128014000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:128003000-128016400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:128003400-128014000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:128003600-128013000	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:128003600-128013400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:128004000-128012400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:128004000-128012600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:128004000-128012800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:128004000-128012800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:128004000-128013000	Weak transcription	Dnd41	blood
20	chr2:128004000-128013400	Weak transcription	Thymus	Thymus
21	chr2:128004200-128012000	Weak transcription	Osteobl	bone
22	chr2:128004200-128014000	Weak transcription	Fetal Lung	lung
23	chr2:128004400-128013000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:128004400-128013400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:128004400-128014200	Weak transcription	Primary B cells from cord blood	blood
26	chr2:128004600-128013400	Weak transcription	Placenta	Placenta
27	chr2:128004800-128014000	Weak transcription	Fetal Thymus	thymus
28	chr2:128005000-128014400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:128005000-128016400	Weak transcription	Fetal Kidney	kidney
30	chr2:128005200-128013400	Weak transcription	Spleen	Spleen
31	chr2:128005200-128014000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:128005400-128013400	Weak transcription	Esophagus	oesophagus
33	chr2:128005400-128016200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:128005600-128012200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:128005600-128013200	Weak transcription	Ovary	ovary
36	chr2:128006000-128013400	Weak transcription	Fetal Stomach	stomach
37	chr2:128006200-128013000	Weak transcription	Primary T cells from cord blood	blood

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