Variant report

Variant	rs1353624
Chromosome Location	chr4:143295246-143295247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10009855	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10017259	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10017642	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018876	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10428305	0.84[GIH][hapmap]
rs11723890	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11726659	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12499068	0.90[GIH][hapmap]
rs12641576	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1391093	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1391094	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1497393	0.84[GIH][hapmap]
rs1497400	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs17016001	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17658809	0.87[GIH][hapmap]
rs1908968	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2200841	0.84[GIH][hapmap]
rs2636669	0.90[CEU][hapmap]
rs28546779	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28664218	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28844598	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4479787	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4496653	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56239324	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62328322	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67102237	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6827918	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6828156	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7666932	0.84[GIH][hapmap]
rs9308150	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs977618	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1353624	ZNF827	cis	parietal	SCAN
rs1353624	NDUFC1	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143273400-143299000	Weak transcription	Left Ventricle	heart
2	chr4:143285200-143298400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr4:143288800-143296200	Weak transcription	A549	lung
4	chr4:143289000-143300600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:143289200-143300000	Weak transcription	NH-A	brain
6	chr4:143290200-143296400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:143290200-143298400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:143290400-143305800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:143290400-143322000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:143290600-143296400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:143290600-143296600	Weak transcription	Primary T cells from cord blood	blood
12	chr4:143290600-143296600	Weak transcription	Dnd41	blood
13	chr4:143290800-143300000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:143291000-143295600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:143291200-143299000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:143292200-143296200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:143293400-143295400	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr4:143293400-143295400	Enhancers	HSMMtube	muscle
19	chr4:143293400-143297000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr4:143293400-143302800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr4:143293600-143295400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:143293600-143296600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:143293600-143297000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:143293800-143295400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:143293800-143295400	Enhancers	NHDF-Ad	bronchial
26	chr4:143293800-143295400	Enhancers	NHLF	lung
27	chr4:143293800-143295600	Enhancers	HMEC	breast
28	chr4:143293800-143295600	Enhancers	HSMM	muscle
29	chr4:143293800-143295600	Enhancers	Osteobl	bone
30	chr4:143293800-143297000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:143293800-143297000	Enhancers	NHEK	skin
32	chr4:143293800-143298000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:143293800-143298400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr4:143294000-143295600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr4:143294000-143297400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:143294200-143295400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:143294200-143295600	Enhancers	Stomach Mucosa	stomach
38	chr4:143294200-143295600	Enhancers	HUVEC	blood vessel
39	chr4:143294200-143296000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:143294200-143296200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr4:143294200-143296200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:143294200-143296200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:143294200-143299600	Weak transcription	Right Ventricle	heart
44	chr4:143294200-143300800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:143294200-143305400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:143294400-143296000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:143294600-143296200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:143294600-143296400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:143294800-143295400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr4:143294800-143296000	Weak transcription	Fetal Heart	heart

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