Variant report

Variant	rs6537745
Chromosome Location	chr1:113154080-113154081
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	chr1:113143142..113146468-chr1:113154015..113156949,3	MCF-7	breast:
2	chr1:113008891..113010966-chr1:113152258..113154210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134245	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

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];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857969	0.94[ASN][1000 genomes]
rs11102494	0.85[EUR][1000 genomes]
rs11102508	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102510	0.95[EUR][1000 genomes]
rs11102517	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12048528	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12118370	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12119489	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126494	0.80[EUR][1000 genomes]
rs12136781	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12137107	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12138335	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12143068	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1238	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12401734	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12402469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12402929	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs12406906	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]
rs12739994	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12750023	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12750621	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12758377	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17438324	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932529	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2932534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932539	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3013433	0.84[EUR][1000 genomes]
rs3013441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34531155	0.93[EUR][1000 genomes]
rs35482634	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36029940	0.85[EUR][1000 genomes]
rs3762335	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3790612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3795820	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4240534	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4838960	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4838961	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61818772	0.85[EUR][1000 genomes]
rs61818800	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537740	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6537742	0.84[CEU][hapmap]
rs6537744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6537746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6537747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6658555	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6659677	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6661642	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6663922	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6668533	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6671645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6672761	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6673930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674053	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674068	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681371	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6682678	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6690169	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6690292	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691025	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691917	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693880	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696991	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698030	0.93[EUR][1000 genomes]
rs6701351	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7415988	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7512984	0.81[ASN][1000 genomes]
rs7516421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7519368	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7522110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7527076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7537789	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7542820	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7546203	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549547	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7551933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552692	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9429694	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662162	0.87[ASN][1000 genomes]
rs999923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[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	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
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6537745	ST7L	cis	Nerve Tibial	GTEx
rs6537745	ST7L	cis	multi-tissue	Pritchard
rs6537745	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs6537745	ST7L	cis	lung	GTEx
rs6537745	ST7L	cis	Lymphoblastoid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113109000-113160000	Weak transcription	Gastric	stomach
2	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
3	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
4	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
5	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
9	chr1:113132600-113154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
12	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:113133200-113159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:113133200-113159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:113135400-113159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:113136200-113156800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:113136600-113158800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:113136800-113159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:113137000-113154200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:113138000-113159400	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:113139200-113159600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:113140200-113159200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:113140400-113160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:113140600-113159200	Strong transcription	Fetal Stomach	stomach
26	chr1:113144000-113158600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:113144000-113160800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:113145000-113159600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:113145800-113159400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:113146200-113156000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr1:113146800-113159000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:113147800-113158400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:113148200-113156600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:113148200-113156800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:113148200-113156800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:113148200-113158400	Strong transcription	Brain Germinal Matrix	brain
37	chr1:113148200-113158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:113148200-113158800	Strong transcription	Liver	Liver
39	chr1:113148200-113158800	Strong transcription	Dnd41	blood
40	chr1:113148200-113159000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:113148200-113159000	Strong transcription	Placenta	Placenta
42	chr1:113148200-113159200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:113148200-113159800	Strong transcription	Fetal Intestine Small	intestine
44	chr1:113148400-113156800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:113148400-113157000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:113148400-113158600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:113148400-113158600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:113148400-113158800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr1:113148400-113158800	Strong transcription	Adipose Nuclei	Adipose
50	chr1:113148400-113158800	Strong transcription	Osteobl	bone

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