Variant report

Variant	rs12140058
Chromosome Location	chr1:10049177-10049178
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10779734	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11121510	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11121512	0.96[ASN][1000 genomes]
rs11828	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12140009	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12140015	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1220389	0.86[ASN][1000 genomes]
rs1220397	1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1220398	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs1220399	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1220400	0.88[ASN][1000 genomes]
rs1220402	0.89[ASN][1000 genomes]
rs1220420	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1220421	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1220424	0.89[ASN][1000 genomes]
rs1234694	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1628143	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1660733	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2890358	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2919694	0.85[ASN][1000 genomes]
rs3003376	0.81[ASW][hapmap];0.84[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3003377	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3003378	0.86[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3013783	0.85[ASN][1000 genomes]
rs3013784	0.91[ASN][1000 genomes]
rs3013788	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3123522	0.84[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58528460	0.82[ASN][1000 genomes]
rs6541073	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661806	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664631	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6678023	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6680076	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7517360	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517806	0.88[ASN][1000 genomes]
rs7517812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7528979	0.81[ASW][hapmap];0.85[CEU][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs7539191	0.92[ASN][1000 genomes]
rs7539725	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12140058	MTHFR	cis	cerebellum	SCAN
rs12140058	HES3	cis	cerebellum	SCAN
rs12140058	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs12140058	LZIC	cis	Lymphoblastoid	GTEx
rs12140058	LZIC	cis	multi-tissue	Pritchard
rs12140058	LZIC	cis	lymphoblastoid	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10028400-10050000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:10032800-10057000	Weak transcription	Psoas Muscle	Psoas
3	chr1:10035600-10051800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:10036000-10050400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:10036800-10051200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:10037200-10054600	Weak transcription	Fetal Brain Female	brain
7	chr1:10039400-10050800	Weak transcription	Colonic Mucosa	Colon
8	chr1:10039600-10053600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:10041000-10049200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:10042600-10050200	Weak transcription	Lung	lung
11	chr1:10042600-10050800	Weak transcription	GM12878-XiMat	blood
12	chr1:10042600-10053800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:10042800-10049800	Weak transcription	Placenta	Placenta
14	chr1:10042800-10049800	Weak transcription	Right Ventricle	heart
15	chr1:10042800-10050200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:10042800-10050600	Weak transcription	Pancreas	Pancrea
17	chr1:10042800-10050800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:10042800-10051200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:10042800-10051200	Weak transcription	HSMMtube	muscle
20	chr1:10042800-10051600	Weak transcription	Fetal Thymus	thymus
21	chr1:10042800-10051600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:10042800-10053000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:10042800-10055600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:10042800-10056600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:10042800-10057200	Weak transcription	Gastric	stomach
26	chr1:10043000-10050400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:10043000-10050600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:10044200-10049600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:10044200-10049600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:10044200-10050000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:10044200-10050000	Weak transcription	Left Ventricle	heart
32	chr1:10044200-10050400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:10044200-10050400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:10044200-10050600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:10044200-10050800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:10044400-10049800	Weak transcription	Spleen	Spleen
37	chr1:10044400-10050200	Weak transcription	Primary T cells from cord blood	blood
38	chr1:10044600-10049600	Weak transcription	Adipose Nuclei	Adipose
39	chr1:10044600-10050000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:10044600-10050800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:10044600-10054800	Weak transcription	Fetal Intestine Large	intestine
42	chr1:10044800-10051000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr1:10044800-10056000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:10045200-10050000	Weak transcription	Primary B cells from cord blood	blood
45	chr1:10045200-10050000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:10045200-10053200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:10045400-10050000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:10045400-10050200	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:10045400-10050600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:10045400-10051600	Weak transcription	Duodenum Mucosa	Duodenum

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