Variant report

Variant	rs13139522
Chromosome Location	chr4:8400643-8400644
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	chr4:8395997..8397565-chr4:8399948..8402070,2	K562	blood:

Variant related genes	Relation type
ENSG00000087008	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10016221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10017177	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1006113	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10938710	0.87[ASN][1000 genomes]
rs10938712	0.99[ASN][1000 genomes]
rs11721377	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs11724408	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11731308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11931965	0.98[ASN][1000 genomes]
rs11934603	0.86[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11938364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103946	0.94[ASN][1000 genomes]
rs13107329	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13130336	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13134272	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13136987	0.92[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13150818	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568692	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1568693	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs2242483	0.93[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2293229	0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs2386119	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs28637781	0.98[ASN][1000 genomes]
rs28805000	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34947973	0.95[ASN][1000 genomes]
rs35893558	0.95[ASN][1000 genomes]
rs3796740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4543095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447868	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs73087705	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7668735	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7696306	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9291391	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9291392	0.96[ASN][1000 genomes]
rs950306	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv878609	chr4:8373832-8407406	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv593639	chr4:8394376-8424108	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13139522	RP11-689P11.2	cis	Artery Tibial	GTEx
rs13139522	EVC2	cis	cerebellum	SCAN
rs13139522	PPP2R2C	cis	cerebellum	SCAN
rs13139522	C4orf23	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr4:8373400-8401600	Strong transcription	Fetal Intestine Small	intestine
3	chr4:8375000-8401600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:8382400-8401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:8384800-8401600	Strong transcription	Thymus	Thymus
7	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
8	chr4:8385200-8411600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:8385600-8407000	Weak transcription	Stomach Mucosa	stomach
10	chr4:8386400-8408400	Strong transcription	Fetal Intestine Large	intestine
11	chr4:8387400-8412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:8389800-8411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:8391200-8406400	Weak transcription	Fetal Thymus	thymus
14	chr4:8393600-8401600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:8393600-8401800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:8393800-8401400	Strong transcription	Gastric	stomach
17	chr4:8394000-8401600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:8394200-8407400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:8394800-8403200	Weak transcription	Psoas Muscle	Psoas
20	chr4:8394800-8409400	Weak transcription	Small Intestine	intestine
21	chr4:8395800-8411800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:8396000-8401400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:8396000-8401400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:8396400-8404800	Weak transcription	A549	lung
25	chr4:8396400-8405800	Weak transcription	GM12878-XiMat	blood
26	chr4:8396600-8401600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr4:8396600-8401600	Strong transcription	Adipose Nuclei	Adipose
28	chr4:8396600-8401600	Strong transcription	Duodenum Mucosa	Duodenum
29	chr4:8396600-8404000	Weak transcription	HUVEC	blood vessel
30	chr4:8396600-8404400	Weak transcription	Fetal Kidney	kidney
31	chr4:8396600-8407200	Weak transcription	Dnd41	blood
32	chr4:8396600-8419400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:8396800-8401400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:8396800-8401400	Strong transcription	Esophagus	oesophagus
35	chr4:8396800-8401400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:8396800-8401600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:8396800-8403400	Weak transcription	Right Atrium	heart
38	chr4:8396800-8412400	Weak transcription	Fetal Brain Male	brain
39	chr4:8396800-8415600	Weak transcription	NH-A	brain
40	chr4:8397000-8400800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:8397000-8401000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:8397000-8401400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:8397000-8401400	Strong transcription	Lung	lung
44	chr4:8397000-8401400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr4:8397000-8406600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:8397200-8401600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:8397400-8401600	Strong transcription	Aorta	Aorta
48	chr4:8397400-8401600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:8397600-8401400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:8397600-8401600	Strong transcription	Colon Smooth Muscle	Colon

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