Variant report

Variant	rs7586672
Chromosome Location	chr2:128223875-128223876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr2:128223768-128223983	HepG2	liver:	n/a	chr2:128223885-128223896
2	USF1	chr2:128223700-128224072	K562	blood:	n/a	chr2:128223885-128223896
3	USF1	chr2:128223715-128224033	ECC-1	luminal epithelium:	n/a	chr2:128223885-128223896

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128223739..128227371-chr2:128227403..128230155,4	K562	blood:
2	chr2:128223739..128227156-chr2:128228484..128231083,5	K562	blood:

Variant related genes	Relation type
ENSG00000231731	TF binding region
ENSG00000202429	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10201047	0.84[EUR][1000 genomes]
rs10496663	0.87[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[LWK][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10928765	0.82[CEU][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes]
rs10928766	0.82[EUR][1000 genomes]
rs10928769	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11679431	0.94[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11680815	0.82[EUR][1000 genomes]
rs11681225	0.94[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11682864	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11685630	0.86[CHB][hapmap]
rs11688201	0.83[CHB][hapmap]
rs11690086	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11892245	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11900469	0.82[EUR][1000 genomes]
rs12053309	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12233101	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12616200	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12618494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619972	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12620037	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12623334	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13011041	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13389029	0.93[EUR][1000 genomes]
rs1568277	0.81[EUR][1000 genomes]
rs1568279	0.82[EUR][1000 genomes]
rs17015274	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17015334	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1864553	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs2082182	0.94[CHB][hapmap];0.85[CHD][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap]
rs2099209	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs2288655	0.94[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3732205	0.83[CHB][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3889307	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56100618	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56106399	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56261855	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56327685	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58880408	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62160265	0.82[EUR][1000 genomes]
rs62160266	0.82[EUR][1000 genomes]
rs62160287	0.84[EUR][1000 genomes]
rs62160288	0.84[EUR][1000 genomes]
rs62160289	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62160291	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66609069	0.86[EUR][1000 genomes]
rs6716489	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67495946	0.81[EUR][1000 genomes]
rs6758364	0.87[CHB][hapmap]
rs777556	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs873099	0.88[CHB][hapmap];0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	esv3458275	chr2:128223577-128225946	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3458278	chr2:128223611-128225916	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3458277	chr2:128223628-128225864	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3458276	chr2:128223678-128225829	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3458279	chr2:128223692-128225828	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv11314	chr2:128223693-128225835	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv516410	chr2:128223875-128225228	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv3693423	chr2:128223875-128230794	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7586672	AC068282.3	cis	Nerve Tibial	GTEx
rs7586672	MAP3K2	cis	multi-tissue	Pritchard
rs7586672	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs7586672	AC068282.3	cis	Heart Left Ventricle	GTEx
rs7586672	AC068282.3	cis	Artery Tibial	GTEx
rs7586672	AC068282.3	cis	Whole Blood	GTEx
rs7586672	GYPC	cis	parietal	SCAN
rs7586672	AC068282.3	cis	Esophagus Muscularis	GTEx
rs7586672	AC068282.3	cis	Muscle Skeletal	GTEx
rs7586672	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7586672	AC068282.3	cis	Thyroid	GTEx
rs7586672	AC068282.3	cis	lung	GTEx
rs7586672	AC068282.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128204800-128225600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:128206000-128224000	Weak transcription	Psoas Muscle	Psoas
3	chr2:128206200-128237800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:128206800-128233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:128208400-128238800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:128208800-128226000	Weak transcription	Brain Anterior Caudate	brain
7	chr2:128209000-128238000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:128209200-128225400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:128209200-128237600	Weak transcription	Adipose Nuclei	Adipose
10	chr2:128210000-128226400	Weak transcription	Esophagus	oesophagus
11	chr2:128210000-128227200	Weak transcription	Left Ventricle	heart
12	chr2:128210000-128237600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:128210200-128238000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:128210600-128225200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:128211200-128225400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:128211200-128225600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:128211400-128226600	Weak transcription	Ovary	ovary
18	chr2:128211600-128226800	Weak transcription	Brain Angular Gyrus	brain
19	chr2:128211600-128227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:128211600-128237600	Weak transcription	Right Ventricle	heart
21	chr2:128212200-128226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:128213000-128237600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:128213200-128225400	Weak transcription	Dnd41	blood
24	chr2:128213200-128237800	Weak transcription	Colonic Mucosa	Colon
25	chr2:128213400-128237800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:128213600-128225200	Weak transcription	A549	lung
27	chr2:128213600-128225400	Weak transcription	Pancreas	Pancrea
28	chr2:128213600-128226600	Weak transcription	Gastric	stomach
29	chr2:128213600-128237600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:128213600-128237800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:128213800-128238000	Weak transcription	Brain Germinal Matrix	brain
32	chr2:128215400-128225200	Weak transcription	Liver	Liver
33	chr2:128215400-128226800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:128216200-128233600	Weak transcription	GM12878-XiMat	blood
35	chr2:128219800-128237600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:128220400-128239800	Weak transcription	Fetal Lung	lung
37	chr2:128221200-128224400	Enhancers	Fetal Intestine Large	intestine
38	chr2:128221400-128226600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:128221600-128224800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:128221600-128226600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:128221600-128226800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:128221600-128227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:128221600-128229000	Weak transcription	HepG2	liver
44	chr2:128221600-128230200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:128221600-128237400	Weak transcription	HSMM	muscle
46	chr2:128221600-128237600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:128222000-128224000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:128222000-128224000	Weak transcription	Fetal Stomach	stomach
49	chr2:128222200-128224000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr2:128222200-128224000	Enhancers	Fetal Intestine Small	intestine

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