Variant report

Variant	rs12118913
Chromosome Location	chr1:197512404-197512405
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	chr1:197507241..197510211-chr1:197512061..197514792,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10801605	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10922215	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10922216	0.88[JPT][hapmap]
rs10922221	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10922223	1.00[JPT][hapmap]
rs10922225	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10922247	0.86[ASN][1000 genomes]
rs10922249	0.97[ASN][1000 genomes]
rs11583319	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11588864	0.81[AMR][1000 genomes]
rs11799515	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11802794	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12117045	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs12118513	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12131588	0.81[AMR][1000 genomes]
rs12141028	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12142127	0.83[ASN][1000 genomes]
rs12354257	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs12724239	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12748009	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1421399	0.83[ASN][1000 genomes]
rs16841842	0.87[AMR][1000 genomes]
rs16841904	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs16841912	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs17621130	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17641524	0.82[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs1775452	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2042097	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2476020	0.89[CHD][hapmap];0.88[JPT][hapmap]
rs2477077	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs2488389	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs2488397	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2488398	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2488401	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs2494268	0.88[JPT][hapmap]
rs2759662	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs2759663	0.88[JPT][hapmap]
rs2821102	0.88[JPT][hapmap]
rs2821121	0.89[CHD][hapmap];0.88[JPT][hapmap]
rs2884629	0.84[ASN][1000 genomes]
rs35624964	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35939830	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6702421	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7522325	0.86[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521647	chr1:197464448-197529218	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12118913	RGS2	cis	parietal	SCAN
rs12118913	DENND1B	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197478000-197541200	Weak transcription	Aorta	Aorta
2	chr1:197480000-197535800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:197480200-197541200	Weak transcription	Esophagus	oesophagus
4	chr1:197480200-197541200	Weak transcription	Fetal Thymus	thymus
5	chr1:197480400-197541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:197481200-197513400	Weak transcription	Adipose Nuclei	Adipose
7	chr1:197481400-197529600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:197487800-197536000	Weak transcription	Fetal Lung	lung
9	chr1:197491600-197520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:197496200-197532400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:197500600-197529400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:197502200-197531800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:197502400-197534600	Weak transcription	Fetal Intestine Large	intestine
14	chr1:197503200-197524000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:197503200-197526400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:197503200-197541200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:197503600-197514400	Weak transcription	Right Ventricle	heart
18	chr1:197503600-197535800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:197504200-197529000	Weak transcription	Fetal Intestine Small	intestine
20	chr1:197505400-197532400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:197505600-197541000	Weak transcription	Pancreas	Pancrea
22	chr1:197506000-197513800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:197506200-197526000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:197506400-197535800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:197506600-197537600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:197506800-197535600	Weak transcription	Primary B cells from cord blood	blood
27	chr1:197506800-197564600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:197507200-197519000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:197508400-197522400	Weak transcription	Dnd41	blood
30	chr1:197508400-197602400	Weak transcription	Left Ventricle	heart
31	chr1:197508600-197528400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:197508600-197532200	Weak transcription	Primary T cells from cord blood	blood
33	chr1:197509000-197514000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr1:197509000-197529600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:197509200-197529200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:197509200-197529600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:197509200-197535600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:197509200-197535600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr1:197509400-197513800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:197509400-197536000	Weak transcription	Liver	Liver
41	chr1:197510200-197513800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:197511400-197535800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:197511800-197535600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:197512000-197529400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:197512400-197512800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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