Variant report

Variant	rs2932536
Chromosome Location	chr1:113202417-113202418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113202278..113203870-chr1:113207719..113210666,2	MCF-7	breast:
2	chr1:113201056..113203899-chr1:113214909..113217826,3	MCF-7	breast:
3	chr1:113202139..113204725-chr1:113211463..113213311,2	MCF-7	breast:
4	chr1:113201703..113204472-chr1:113215980..113217663,2	MCF-7	breast:
5	chr1:113160231..113165111-chr1:113199772..113204361,6	K562	blood:
6	chr1:113202189..113204347-chr1:113247857..113249740,2	K562	blood:
7	chr1:113161290..113166205-chr1:113202246..113206861,5	K562	blood:

Variant related genes	Relation type
ENSG00000155366	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001494	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10745330	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs10776755	0.89[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs10776757	0.89[CEU][hapmap]
rs10857963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs11102497	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11102512	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11584092	0.88[CEU][hapmap]
rs12046208	0.88[CEU][hapmap];0.83[GIH][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap]
rs12046329	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046466	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12126277	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12728001	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs1994604	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932532	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999154	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999155	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999157	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3013431	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3013439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3013440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103450	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351372	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs4838959	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs4839254	0.84[CEU][hapmap]
rs6537743	0.82[EUR][1000 genomes]
rs6537748	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs6537749	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs6666579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6669096	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6682737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6691932	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6700673	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7415820	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7513716	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs7522288	0.81[CEU][hapmap]
rs7524494	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7544663	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs7546094	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7554345	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7554916	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs902289	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs910697	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs9429486	0.88[CEU][hapmap]
rs954679	0.95[JPT][hapmap]

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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2932536	ST7L	cis	Lymphoblastoid	GTEx
rs2932536	ST7L	cis	Esophagus Muscularis	GTEx
rs2932536	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs2932536	C1orf162	cis	parietal	SCAN
rs2932536	ST7L	cis	Heart Left Ventricle	GTEx
rs2932536	ST7L	cis	Adipose Subcutaneous	GTEx
rs2932536	ST7L	cis	Thyroid	GTEx
rs2932536	ST7L	cis	normal skin	skin_eQTL
rs2932536	ST7L	cis	lymphoblastoid	seeQTL
rs2932536	ST7L	cis	Nerve Tibial	GTEx
rs2932536	ST7L	cis	uninvolved skin	skin_eQTL
rs2932536	ST7L	cis	lung	GTEx
rs2932536	ST7L	cis	multi-tissue	Pritchard
rs2932536	SYCP1	cis	parietal	SCAN
rs2932536	ST7L	cis	lesional skin	skin_eQTL
rs2932536	ALX3	cis	parietal	SCAN
rs2932536	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs2932536	WNT2B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
2	chr1:113168800-113215800	Weak transcription	Fetal Heart	heart
3	chr1:113179000-113215600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:113180000-113216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:113180200-113203000	Weak transcription	Aorta	Aorta
6	chr1:113184200-113215600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:113184600-113214800	Strong transcription	Hela-S3	cervix
8	chr1:113185000-113214800	Strong transcription	Dnd41	blood
9	chr1:113185400-113216200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:113186000-113210800	Strong transcription	GM12878-XiMat	blood
11	chr1:113186000-113214800	Strong transcription	Fetal Thymus	thymus
12	chr1:113186000-113215000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:113186200-113215400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:113187000-113213200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:113187000-113215200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:113187200-113215200	Strong transcription	HSMM	muscle
17	chr1:113187400-113215000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:113187800-113202800	Weak transcription	Small Intestine	intestine
19	chr1:113187800-113204000	Weak transcription	Right Ventricle	heart
20	chr1:113187800-113216000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:113188400-113215000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:113188800-113213800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:113189000-113213800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:113189200-113203600	Weak transcription	Gastric	stomach
25	chr1:113189200-113203800	Weak transcription	Pancreas	Pancrea
26	chr1:113189200-113211000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:113189200-113214600	Strong transcription	NHEK	skin
28	chr1:113189200-113214800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:113189200-113215000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:113189400-113214800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:113189800-113213800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:113189800-113215200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:113189800-113215400	Strong transcription	Placenta	Placenta
34	chr1:113189800-113216200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:113190000-113210600	Strong transcription	Primary B cells from cord blood	blood
36	chr1:113190000-113214600	Strong transcription	Liver	Liver
37	chr1:113190000-113215200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:113190000-113215200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:113190000-113215200	Strong transcription	NH-A	brain
40	chr1:113190000-113215400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:113190000-113215400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:113190200-113210600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:113190200-113214400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr1:113190200-113214600	Strong transcription	Adipose Nuclei	Adipose
45	chr1:113190600-113211000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:113190600-113213000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:113190600-113214200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:113190800-113209000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:113190800-113215000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr1:113191000-113213600	Strong transcription	Primary T cells from cord blood	blood

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