Variant report

Variant	rs4150434
Chromosome Location	chr2:128042100-128042101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128041472..128042991-chr2:128051004..128053576,3	MCF-7	breast:
2	chr2:128039289..128042277-chr2:128174042..128176143,2	MCF-7	breast:
3	chr2:128041948..128047120-chr2:128049518..128053059,6	MCF-7	breast:
4	chr2:128014970..128016658-chr2:128040574..128042707,2	MCF-7	breast:
5	chr2:128023647..128026274-chr2:128041250..128043477,2	K562	blood:
6	chr2:128040423..128043737-chr2:128045264..128047560,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163161	Chromatin interaction
ENSG00000115718	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10167294	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10928764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1143407	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684068	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11899601	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12613252	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613254	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614320	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12617858	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619391	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017103	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13034157	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13390029	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13403918	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409933	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13414676	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13429925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2139142	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276683	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28807127	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3088374	0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs34006114	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34441363	0.90[EUR][1000 genomes]
rs34487399	0.91[EUR][1000 genomes]
rs34601617	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34703177	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs35708549	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893313	0.93[EUR][1000 genomes]
rs4150492	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150514	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300780	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4359587	0.93[EUR][1000 genomes]
rs4528711	0.88[EUR][1000 genomes]
rs4662721	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4662724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58063879	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59027829	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6430937	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6716392	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]
rs6735779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6738811	0.89[EUR][1000 genomes]
rs6747862	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6752139	0.89[EUR][1000 genomes]
rs6761391	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs67771362	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7584659	0.81[ASN][1000 genomes]
rs9752366	0.84[EUR][1000 genomes]
rs9923	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	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
2	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4150434	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4150434	MAP3K2	cis	Brain Pons	GTEx
rs4150434	MAP3K2	cis	Cerebellum	GTEx
rs4150434	AC068282.3	cis	Muscle Skeletal	GTEx
rs4150434	AC068282.3	cis	Esophagus Muscularis	GTEx
rs4150434	AC068282.3	cis	Nerve Tibial	GTEx
rs4150434	AC068282.3	cis	Esophagus Mucosa	GTEx
rs4150434	AC068282.3	cis	Whole Blood	GTEx
rs4150434	AC068282.3	cis	Artery Tibial	GTEx
rs4150434	AC068282.3	cis	Stomach	GTEx
rs4150434	AC068282.3	cis	Artery Aorta	GTEx
rs4150434	AC068282.3	cis	Thyroid	GTEx
rs4150434	MAP3K2	cis	multi-tissue	Pritchard
rs4150434	AC068282.3	cis	Heart Left Ventricle	GTEx
rs4150434	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs4150434	MAP3K2	cis	Temporal Cortex	GTEx
rs4150434	MAP3K2	cis	Frontal Cortex	GTEx
rs4150434	AC068282.3	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128021200-128050000	Strong transcription	Fetal Stomach	stomach
2	chr2:128023400-128050400	Strong transcription	Liver	Liver
3	chr2:128024200-128050600	Strong transcription	Fetal Intestine Large	intestine
4	chr2:128024400-128049600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr2:128024400-128049800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:128024400-128050000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:128024400-128050200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:128024400-128050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:128024400-128050200	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:128024400-128050400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:128024400-128050400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:128024400-128050400	Strong transcription	Thymus	Thymus
13	chr2:128024400-128050800	Strong transcription	Fetal Thymus	thymus
14	chr2:128024600-128049200	Strong transcription	Dnd41	blood
15	chr2:128024600-128049600	Strong transcription	Primary T cells from cord blood	blood
16	chr2:128024600-128050000	Strong transcription	HepG2	liver
17	chr2:128024600-128050200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:128024600-128050200	Strong transcription	Adipose Nuclei	Adipose
19	chr2:128024800-128044200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:128024800-128050000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr2:128024800-128050200	Strong transcription	Brain Anterior Caudate	brain
22	chr2:128024800-128050200	Strong transcription	Brain Hippocampus Middle	brain
23	chr2:128024800-128050200	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:128024800-128050200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr2:128024800-128050400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:128024800-128050400	Strong transcription	Osteobl	bone
27	chr2:128025000-128050600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:128025200-128050000	Strong transcription	Left Ventricle	heart
29	chr2:128025200-128050200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:128025800-128050000	Strong transcription	Spleen	Spleen
31	chr2:128028200-128042200	Strong transcription	NHLF	lung
32	chr2:128028400-128044400	Weak transcription	Stomach Mucosa	stomach
33	chr2:128032400-128048200	Strong transcription	Rectal Smooth Muscle	rectum
34	chr2:128032600-128042600	Strong transcription	HSMM	muscle
35	chr2:128033400-128042200	Strong transcription	Aorta	Aorta
36	chr2:128033800-128050400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:128034200-128050200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:128034200-128050200	Strong transcription	K562	blood
39	chr2:128034400-128050000	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr2:128034400-128050200	Strong transcription	HUVEC	blood vessel
41	chr2:128034800-128050400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:128036000-128048600	Strong transcription	HSMMtube	muscle
43	chr2:128036600-128050200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:128036600-128050800	Weak transcription	Right Atrium	heart
45	chr2:128036800-128050200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:128037400-128050400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:128037400-128050400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:128037400-128050600	Strong transcription	Right Ventricle	heart
49	chr2:128039200-128050000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:128039200-128050200	Strong transcription	Brain Substantia Nigra	brain

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