Variant report

Variant	rs7636909
Chromosome Location	chr3:142260562-142260563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142246869..142249118-chr3:142259250..142261613,2	K562	blood:
2	chr3:142255246..142257071-chr3:142259760..142261943,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1129391	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708470	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11718899	0.82[ASN][1000 genomes]
rs11916455	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923612	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12629001	0.83[ASN][1000 genomes]
rs12629713	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634255	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12638158	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12639363	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13063075	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13065800	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13066441	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13068397	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13070239	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072346	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13072355	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13082648	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs13085247	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13085261	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13089219	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13092234	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13093304	0.82[ASN][1000 genomes]
rs13099184	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs2227929	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227931	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306699	0.95[CHB][hapmap]
rs34392719	0.81[GIH][hapmap]
rs3923464	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4256152	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4558780	0.81[ASN][1000 genomes]
rs4582075	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs57299906	0.83[EUR][1000 genomes]
rs6440085	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6776402	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6786320	0.94[CHB][hapmap]
rs7432464	0.82[ASN][1000 genomes]
rs7623785	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs7630115	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7641914	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7643377	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs7647329	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs953135	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs9814159	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs9829125	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs9859834	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs9867210	0.95[CHB][hapmap];0.97[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer 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 target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7636909	XRN1	cis	cerebellum	SCAN
rs7636909	PLS1	cis	parietal	SCAN
rs7636909	TRPC1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
3	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
5	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
6	chr3:142209400-142271800	Weak transcription	HepG2	liver
7	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
8	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
9	chr3:142233600-142271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:142238600-142269000	Weak transcription	Fetal Intestine Small	intestine
11	chr3:142239800-142269600	Weak transcription	Thymus	Thymus
12	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
13	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:142241800-142270800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:142242400-142275800	Weak transcription	NHEK	skin
16	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
17	chr3:142248400-142269000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:142248600-142273600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:142250400-142261600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:142251000-142262200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:142251600-142264800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:142251800-142270800	Weak transcription	Fetal Kidney	kidney
24	chr3:142251800-142271600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:142253200-142260800	Weak transcription	Left Ventricle	heart
26	chr3:142253200-142262200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:142253200-142264000	Weak transcription	Fetal Brain Female	brain
28	chr3:142253200-142264400	Weak transcription	Brain Germinal Matrix	brain
29	chr3:142253200-142264400	Weak transcription	Fetal Lung	lung
30	chr3:142253200-142269600	Weak transcription	Pancreas	Pancrea
31	chr3:142253200-142271200	Weak transcription	Psoas Muscle	Psoas
32	chr3:142253200-142271800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:142253400-142268000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:142253400-142268400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:142253400-142270200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:142253400-142270600	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:142253400-142270800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:142253400-142284800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:142253400-142284800	Weak transcription	Brain Substantia Nigra	brain
40	chr3:142253600-142267600	Weak transcription	Brain Anterior Caudate	brain
41	chr3:142253600-142268400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:142253600-142271600	Weak transcription	Brain Angular Gyrus	brain
43	chr3:142253800-142263400	Weak transcription	HMEC	breast
44	chr3:142253800-142296400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:142254000-142270000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:142254200-142265400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:142254200-142268400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:142254800-142260600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:142255000-142268400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:142255400-142265400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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