Variant report

Variant	rs6537748
Chromosome Location	chr1:113214381-113214382
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113214019-113219584	K562	blood:	n/a	n/a
2	POLR2A	chr1:113214290-113214552	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:113214356-113214779	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:113214306-113214796	K562	blood:	n/a	n/a
5	POLR2A	chr1:113214313-113214693	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:113214234-113217824	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:113214315-113214768	K562	blood:	n/a	n/a
8	POLR2A	chr1:113214365-113217673	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113211024..113213434-chr1:113214018..113215567,2	K562	blood:
2	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:

Variant related genes	Relation type
MOV10	TF binding region
ENSG00000155363	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000225075	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10745330	0.81[GIH][hapmap]
rs10776755	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs10776757	0.85[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs1110043	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584092	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042407	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12046208	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932532	0.87[TSI][hapmap]
rs2932536	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs2999154	0.85[TSI][hapmap]
rs2999155	0.87[TSI][hapmap]
rs2999156	0.89[GIH][hapmap]
rs351372	0.81[GIH][hapmap]
rs4838959	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs4839254	0.82[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs55675817	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537749	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6666579	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs6682737	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs6700673	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs72699100	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7415820	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs7522288	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544663	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs7554916	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs902289	0.87[TSI][hapmap]
rs937053	0.96[ASN][1000 genomes]
rs9429486	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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	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
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6537748	ST7L	cis	lung	GTEx
rs6537748	WNT2B	cis	parietal	SCAN
rs6537748	C1orf162	cis	parietal	SCAN
rs6537748	KCNA10	cis	parietal	SCAN
rs6537748	ST7L	cis	lymphoblastoid	seeQTL
rs6537748	ST7L	cis	uninvolved skin	skin_eQTL
rs6537748	ST7L	cis	normal skin	skin_eQTL
rs6537748	ST7L	cis	multi-tissue	Pritchard
rs6537748	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs6537748	ST7L	cis	Artery Tibial	GTEx
rs6537748	SYCP1	cis	parietal	SCAN
rs6537748	ST7L	cis	Thyroid	GTEx
rs6537748	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113168800-113215800	Weak transcription	Fetal Heart	heart
2	chr1:113179000-113215600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:113180000-113216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:113184200-113215600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:113184600-113214800	Strong transcription	Hela-S3	cervix
6	chr1:113185000-113214800	Strong transcription	Dnd41	blood
7	chr1:113185400-113216200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:113186000-113214800	Strong transcription	Fetal Thymus	thymus
9	chr1:113186000-113215000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:113186200-113215400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:113187000-113215200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:113187200-113215200	Strong transcription	HSMM	muscle
13	chr1:113187400-113215000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:113187800-113216000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:113188400-113215000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:113189200-113214600	Strong transcription	NHEK	skin
17	chr1:113189200-113214800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:113189200-113215000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:113189400-113214800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:113189800-113215200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:113189800-113215400	Strong transcription	Placenta	Placenta
22	chr1:113189800-113216200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:113190000-113214600	Strong transcription	Liver	Liver
24	chr1:113190000-113215200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:113190000-113215200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:113190000-113215200	Strong transcription	NH-A	brain
27	chr1:113190000-113215400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:113190000-113215400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:113190200-113214400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:113190200-113214600	Strong transcription	Adipose Nuclei	Adipose
31	chr1:113190800-113215000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr1:113191000-113215000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:113191400-113215200	Strong transcription	Fetal Intestine Large	intestine
34	chr1:113191600-113214800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:113194400-113216000	Weak transcription	Stomach Mucosa	stomach
36	chr1:113195800-113215200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:113196800-113215200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:113197000-113214400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:113197000-113214800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:113197000-113215000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:113197000-113215400	Strong transcription	Osteobl	bone
42	chr1:113198200-113215200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:113199200-113214600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:113199200-113214800	Strong transcription	HSMMtube	muscle
45	chr1:113199200-113215200	Strong transcription	HUVEC	blood vessel
46	chr1:113199200-113215400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:113199400-113215000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:113199800-113215200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:113203400-113216200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:113204200-113216200	Weak transcription	Pancreas	Pancrea

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