Variant report

Variant	rs12401734
Chromosome Location	chr1:113071834-113071835
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	chr1:113070857..113072562-chr1:113074305..113076208,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10745331	1.00[CEU][hapmap]
rs10745332	1.00[CEU][hapmap]
rs11102494	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11102508	0.84[EUR][1000 genomes]
rs11102510	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048528	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs12119489	0.81[EUR][1000 genomes]
rs12125361	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12136781	0.95[EUR][1000 genomes]
rs12137107	0.86[EUR][1000 genomes]
rs12138335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12143068	0.86[EUR][1000 genomes]
rs12144044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1238	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs12402469	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12402929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406906	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs12739994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12750023	0.89[EUR][1000 genomes]
rs12750621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12758377	0.86[EUR][1000 genomes]
rs17438324	0.95[EUR][1000 genomes]
rs2273369	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2279500	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2932529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2932534	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs2932535	1.00[CEU][hapmap]
rs2932537	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs2932538	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs2932539	1.00[CEU][hapmap]
rs3013441	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs34531155	0.86[EUR][1000 genomes]
rs35482634	0.89[EUR][1000 genomes]
rs36029940	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3762335	0.95[EUR][1000 genomes]
rs3790611	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3790612	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3795820	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4240534	0.81[EUR][1000 genomes]
rs4838960	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs4838961	0.81[EUR][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs61818772	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6537740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537741	1.00[JPT][hapmap]
rs6537742	0.84[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6537744	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6537745	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6537746	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6537747	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs6658555	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6659677	0.95[EUR][1000 genomes]
rs6661642	0.95[EUR][1000 genomes]
rs6663922	0.93[EUR][1000 genomes]
rs6668533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671645	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6672761	0.95[EUR][1000 genomes]
rs6673930	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6674053	0.84[EUR][1000 genomes]
rs6674068	0.85[EUR][1000 genomes]
rs6681371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6682678	0.85[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs6690169	0.89[EUR][1000 genomes]
rs6690292	1.00[CEU][hapmap]
rs6691025	0.83[EUR][1000 genomes]
rs6691917	0.84[EUR][1000 genomes]
rs6693880	0.90[EUR][1000 genomes]
rs6696991	0.93[EUR][1000 genomes]
rs6698030	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6701351	0.84[EUR][1000 genomes]
rs7415988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7516421	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7519368	0.84[ASN][1000 genomes]
rs7522110	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527076	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7535636	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs7537789	0.92[EUR][1000 genomes]
rs7540251	0.86[EUR][1000 genomes]
rs7542820	0.88[EUR][1000 genomes]
rs7546203	0.84[EUR][1000 genomes]
rs7549547	0.95[EUR][1000 genomes]
rs7551933	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs9429694	0.84[EUR][1000 genomes]
rs999923	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12401734	ST7L	cis	multi-tissue	Pritchard
rs12401734	CTTNBP2NL	cis	parietal	SCAN
rs12401734	HBXIP	cis	parietal	SCAN
rs12401734	ST7L	cis	lung	GTEx
rs12401734	ST7L	cis	Nerve Tibial	GTEx
rs12401734	GSTM5	cis	parietal	SCAN
rs12401734	CAPZA1	trans	brain	seeQTL
rs12401734	CAPZA1	cis	brain	seeQTL
rs12401734	ALX3	cis	parietal	SCAN
rs12401734	CAPZA1	cis	lymphoblastoid	seeQTL
rs12401734	FAM102B	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052000-113082600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
3	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
4	chr1:113058400-113086600	Weak transcription	A549	lung
5	chr1:113058800-113119400	Weak transcription	HepG2	liver
6	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
7	chr1:113061200-113072200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:113061400-113081200	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
10	chr1:113063400-113092400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:113065000-113092400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
14	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
15	chr1:113065800-113086200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:113066000-113088800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:113066200-113114400	Weak transcription	Dnd41	blood
20	chr1:113066600-113081200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:113066800-113072800	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:113067000-113083800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
24	chr1:113067600-113072000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:113067600-113072000	Strong transcription	Primary T cells from cord blood	blood
26	chr1:113067800-113079200	Weak transcription	Ovary	ovary
27	chr1:113067800-113083800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr1:113067800-113090200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:113068000-113089600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:113068000-113100200	Weak transcription	Fetal Heart	heart
31	chr1:113068200-113081400	Weak transcription	Fetal Lung	lung
32	chr1:113068400-113074200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:113068600-113086400	Weak transcription	HUVEC	blood vessel
34	chr1:113068800-113081400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:113068800-113087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:113069000-113076600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:113069000-113081600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:113069000-113082800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:113069400-113072600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:113069400-113072600	Enhancers	NHDF-Ad	bronchial
41	chr1:113069400-113072600	Enhancers	NHLF	lung
42	chr1:113069400-113073000	Enhancers	Osteobl	bone
43	chr1:113069600-113072000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:113069600-113072000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:113069800-113072200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:113069800-113072600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:113070000-113073200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:113070200-113072000	Strong transcription	Brain Anterior Caudate	brain
49	chr1:113070200-113073000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:113070200-113082800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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