Variant report

Variant	rs12406906
Chromosome Location	chr1:113117900-113117901
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113117690..113119530-chr1:113159900..113161973,2	K562	blood:

Variant related genes	Relation type
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10745331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10745332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857969	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11102494	0.93[EUR][1000 genomes]
rs11102508	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102510	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11102517	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048528	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.83[ASN][1000 genomes]
rs12118370	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12119489	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12136781	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12137107	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138335	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12143068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs12401734	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs12402469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12402929	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12739994	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12750023	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750621	1.00[CEU][hapmap]
rs12758377	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17438324	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2279500	0.91[GIH][hapmap]
rs2932529	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2932534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.86[ASN][1000 genomes]
rs2932539	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3013441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34531155	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35482634	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36029940	0.93[EUR][1000 genomes]
rs3762335	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3790611	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3790612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795820	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4240534	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4838960	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4838961	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs61818772	0.93[EUR][1000 genomes]
rs61818800	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537740	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6537741	0.81[MEX][hapmap]
rs6537742	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs6537744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658555	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6659677	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661642	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6663922	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668533	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs6671645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672761	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6673930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674053	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674068	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681371	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6682678	0.85[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs6690169	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690292	1.00[CEU][hapmap];0.92[ASN][1000 genomes]
rs6691025	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691917	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693880	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696991	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698030	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6701351	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415988	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7516421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519368	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7522110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7527076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7537789	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540251	0.85[EUR][1000 genomes]
rs7542820	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546203	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549547	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7551933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7552692	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9429694	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9662162	0.84[ASN][1000 genomes]
rs999923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12406906	CAPZA1	cis	lymphoblastoid	seeQTL
rs12406906	RHOC	cis	lymphoblastoid	seeQTL
rs12406906	ST7L	cis	Lymphoblastoid	GTEx
rs12406906	ST7L	cis	lymphoblastoid	seeQTL
rs12406906	HBXIP	cis	parietal	SCAN
rs12406906	ST7L	cis	Nerve Tibial	GTEx
rs12406906	ALX3	cis	parietal	SCAN
rs12406906	ST7L	cis	multi-tissue	Pritchard
rs12406906	CTTNBP2NL	cis	parietal	SCAN
rs12406906	GSTM5	cis	parietal	SCAN
rs12406906	ST7L	cis	lung	GTEx
rs12406906	CAPZA1	cis	brain	seeQTL
rs12406906	CAPZA1	trans	brain	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113058800-113119400	Weak transcription	HepG2	liver
2	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
3	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
6	chr1:113070600-113120200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
8	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
9	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:113082200-113118000	Weak transcription	Lung	lung
12	chr1:113083200-113123200	Weak transcription	Right Atrium	heart
13	chr1:113084000-113131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:113084200-113118000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:113084600-113120600	Weak transcription	Ovary	ovary
16	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:113087600-113125800	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:113088400-113132200	Weak transcription	HMEC	breast
19	chr1:113088800-113118000	Weak transcription	NHEK	skin
20	chr1:113089800-113120400	Weak transcription	Stomach Mucosa	stomach
21	chr1:113092000-113118000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
23	chr1:113100600-113120400	Weak transcription	Fetal Heart	heart
24	chr1:113100600-113120400	Weak transcription	NHLF	lung
25	chr1:113101600-113118000	Weak transcription	NHDF-Ad	bronchial
26	chr1:113103000-113118000	Weak transcription	Brain Substantia Nigra	brain
27	chr1:113105400-113129800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:113109000-113123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:113109000-113160000	Weak transcription	Gastric	stomach
30	chr1:113109200-113118000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:113109400-113118800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:113109400-113122400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:113110200-113119400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:113110800-113118000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:113111000-113131000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:113111800-113138800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:113112000-113128200	Strong transcription	Liver	Liver
39	chr1:113112200-113119000	Strong transcription	Fetal Intestine Small	intestine
40	chr1:113112200-113120400	Weak transcription	Fetal Kidney	kidney
41	chr1:113112600-113131800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:113113200-113124400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr1:113113200-113132400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:113113800-113119800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:113113800-113124400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:113114200-113121800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:113114400-113121200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:113114400-113124600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:113114600-113119600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:113114600-113122000	Strong transcription	Fetal Muscle Leg	muscle

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