Variant report

Variant	rs6716392
Chromosome Location	chr2:128107470-128107471
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	chr2:128107155..128109690-chr2:128143179..128145881,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169967	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10167294	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10928764	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143407	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11684068	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11899601	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12613252	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12613254	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12613413	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614320	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12617858	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12619391	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13017103	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13034157	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13390029	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13403918	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13409933	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13414676	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13429925	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134794	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2139142	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276682	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276683	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28807127	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3088374	0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs34006114	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34441363	0.84[EUR][1000 genomes]
rs34487399	0.86[EUR][1000 genomes]
rs34601617	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34703177	1.00[CEU][hapmap];0.94[GIH][hapmap];0.84[EUR][1000 genomes]
rs35708549	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3738948	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3893313	0.88[EUR][1000 genomes]
rs4150434	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150492	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150506	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150514	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4300780	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4359587	0.88[EUR][1000 genomes]
rs4528711	0.82[EUR][1000 genomes]
rs4662721	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662724	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58063879	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59027829	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6430937	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6735779	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6738811	0.83[EUR][1000 genomes]
rs6747862	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6752139	0.83[EUR][1000 genomes]
rs67771362	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7584659	0.88[ASN][1000 genomes]
rs9923	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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	esv3459771	chr2:128103479-128114160	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv3459772	chr2:128103655-128114047	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6716392	AC068282.3	cis	Muscle Skeletal	GTEx
rs6716392	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6716392	AC068282.3	cis	Esophagus Muscularis	GTEx
rs6716392	MAP3K2	cis	Brain Pons	GTEx
rs6716392	MAP3K2	cis	Frontal Cortex	GTEx
rs6716392	AC068282.3	cis	Artery Aorta	GTEx
rs6716392	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs6716392	AC068282.3	cis	Heart Left Ventricle	GTEx
rs6716392	AC068282.3	cis	Nerve Tibial	GTEx
rs6716392	AC068282.3	cis	lung	GTEx
rs6716392	AC068282.3	cis	Whole Blood	GTEx
rs6716392	AC068282.3	cis	Stomach	GTEx
rs6716392	AC068282.3	cis	Thyroid	GTEx
rs6716392	MAP3K2	cis	multi-tissue	Pritchard
rs6716392	AC068282.3	cis	Esophagus Mucosa	GTEx
rs6716392	AC068282.3	cis	Artery Tibial	GTEx
rs6716392	MAP3K2	cis	Cerebellum	GTEx
rs6716392	MAP3K2	cis	Temporal Cortex	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128059400-128109600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:128069000-128117000	Weak transcription	Small Intestine	intestine
3	chr2:128072200-128109600	Weak transcription	Esophagus	oesophagus
4	chr2:128072200-128111800	Weak transcription	K562	blood
5	chr2:128072600-128112000	Weak transcription	NHEK	skin
6	chr2:128077000-128116200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:128077200-128122800	Weak transcription	Aorta	Aorta
8	chr2:128078600-128109600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:128079400-128107800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:128079800-128107600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:128079800-128114600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:128082000-128114600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:128083600-128117000	Weak transcription	Brain Anterior Caudate	brain
14	chr2:128086600-128112000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:128088800-128109400	Weak transcription	Right Ventricle	heart
16	chr2:128090800-128112000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:128092600-128109400	Weak transcription	Lung	lung
18	chr2:128092600-128122000	Weak transcription	Pancreas	Pancrea
19	chr2:128092800-128109600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:128093200-128122800	Weak transcription	Fetal Kidney	kidney
21	chr2:128095600-128122000	Weak transcription	Brain Angular Gyrus	brain
22	chr2:128096400-128109000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:128096400-128109400	Weak transcription	Ovary	ovary
24	chr2:128096400-128112000	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:128096400-128122200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:128096800-128117800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:128096800-128119600	Weak transcription	HSMM	muscle
28	chr2:128099000-128109400	Weak transcription	Right Atrium	heart
29	chr2:128100000-128112000	Weak transcription	Fetal Lung	lung
30	chr2:128100200-128109600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:128100200-128110000	Weak transcription	Fetal Intestine Large	intestine
32	chr2:128100200-128119600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:128100400-128109400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:128100400-128109400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr2:128100400-128118400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:128100600-128119800	Weak transcription	NHDF-Ad	bronchial
37	chr2:128101600-128116400	Weak transcription	Fetal Thymus	thymus
38	chr2:128101600-128117800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:128102600-128109400	Weak transcription	Left Ventricle	heart
40	chr2:128102600-128122400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:128102800-128109400	Weak transcription	Fetal Intestine Small	intestine
42	chr2:128103600-128109800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr2:128103800-128108600	Weak transcription	Liver	Liver
44	chr2:128103800-128111800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:128104400-128109000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:128104600-128119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:128105400-128108000	Enhancers	Primary B cells from peripheral blood	blood
48	chr2:128105400-128109800	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr2:128105600-128109200	Weak transcription	HepG2	liver
50	chr2:128105600-128127400	Weak transcription	Primary hematopoietic stem cells	blood

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