Variant report

Variant	rs6716724
Chromosome Location	chr2:11510948-11510949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11494304..11496059-chr2:11510335..11513048,2	MCF-7	breast:
2	chr2:11483150..11486998-chr2:11509500..11514812,6	MCF-7	breast:
3	chr2:11483074..11486945-chr2:11508769..11511659,4	MCF-7	breast:
4	chr2:11506369..11508414-chr2:11509960..11513532,3	K562	blood:
5	chr2:11508308..11513224-chr2:11514143..11518077,7	MCF-7	breast:
6	chr2:11509703..11512447-chr2:11679988..11681680,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ROCK2-4	chr2:11510929-11511336	NONHSAT069162

No data

Variant related genes	Relation type
ENSG00000264010	Chromatin interaction
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10170598	0.92[ASN][1000 genomes]
rs10170791	0.88[ASN][1000 genomes]
rs10195908	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202323	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929734	0.87[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12692438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12692439	0.92[ASN][1000 genomes]
rs12692440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12692441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12993210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13024110	0.88[ASW][hapmap];0.86[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35029584	0.92[ASN][1000 genomes]
rs4280434	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4533449	0.92[ASN][1000 genomes]
rs4641909	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4668722	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668723	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6432189	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs6708718	0.92[ASN][1000 genomes]
rs6708945	0.91[ASN][1000 genomes]
rs6711409	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6711414	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6719739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721881	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6756145	0.89[ASN][1000 genomes]
rs7420679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581184	0.86[JPT][hapmap]
rs7595700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Sudden cardiac arrest	21658281	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6716724	PDIA6	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11505400-11514400	Enhancers	Fetal Intestine Large	intestine
2	chr2:11505600-11511600	Enhancers	Fetal Intestine Small	intestine
3	chr2:11505800-11511000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:11506000-11511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:11506000-11514600	Weak transcription	K562	blood
6	chr2:11506800-11511000	Enhancers	HepG2	liver
7	chr2:11507200-11511200	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:11507400-11516200	Enhancers	Stomach Mucosa	stomach
9	chr2:11508400-11513400	Weak transcription	HSMMtube	muscle
10	chr2:11508400-11514800	Weak transcription	Small Intestine	intestine
11	chr2:11508600-11513200	Weak transcription	NH-A	brain
12	chr2:11508600-11513600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:11508600-11514000	Enhancers	Psoas Muscle	Psoas
14	chr2:11508800-11511000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:11508800-11511000	Weak transcription	Fetal Lung	lung
16	chr2:11508800-11511000	Weak transcription	NHLF	lung
17	chr2:11508800-11513200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:11508800-11513400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:11508800-11513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:11508800-11513600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:11508800-11513600	Weak transcription	Osteobl	bone
22	chr2:11508800-11514400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:11508800-11514600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:11508800-11514600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:11508800-11514600	Weak transcription	Right Atrium	heart
26	chr2:11508800-11515000	Weak transcription	Aorta	Aorta
27	chr2:11509000-11513400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:11509000-11514400	Weak transcription	Brain Anterior Caudate	brain
29	chr2:11509000-11514400	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:11509000-11514400	Weak transcription	Brain Substantia Nigra	brain
31	chr2:11509200-11513200	Weak transcription	Left Ventricle	heart
32	chr2:11509200-11514400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:11509200-11514400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:11509400-11511000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr2:11509400-11511200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr2:11509400-11513600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:11509600-11511000	Weak transcription	Fetal Stomach	stomach
38	chr2:11509600-11512200	Enhancers	Colonic Mucosa	Colon
39	chr2:11509600-11513400	Weak transcription	Adipose Nuclei	Adipose
40	chr2:11509600-11513600	Enhancers	Gastric	stomach
41	chr2:11509600-11513800	Weak transcription	Placenta	Placenta
42	chr2:11509800-11512200	Enhancers	A549	lung
43	chr2:11509800-11512400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:11509800-11512800	Weak transcription	Spleen	Spleen
45	chr2:11509800-11513800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:11509800-11514400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:11509800-11514400	Weak transcription	Fetal Brain Male	brain
48	chr2:11510000-11511400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:11510600-11511600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:11510600-11511800	Enhancers	Pancreas	Pancrea

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