Variant report

Variant	rs2932537
Chromosome Location	chr1:113230394-113230395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113183921..113186254-chr1:113229181..113230777,2	MCF-7	breast:
2	chr1:113226289..113228900-chr1:113228989..113230932,2	MCF-7	breast:
3	chr1:113214618..113222446-chr1:113227384..113233520,13	K562	blood:
4	chr1:113217617..113223835-chr1:113226384..113230990,8	MCF-7	breast:
5	chr1:113186005..113187624-chr1:113228785..113231335,2	K562	blood:
6	chr1:113214399..113219266-chr1:113227839..113232151,8	MCF-7	breast:
7	chr1:113229049..113232047-chr1:113233162..113235859,4	MCF-7	breast:
8	chr1:113161141..113162992-chr1:113229521..113231702,2	MCF-7	breast:

No data

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

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12126494	1.00[ASN][1000 genomes]
rs12138335	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12144044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12401734	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs12402929	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12739994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12750621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2279500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2999159	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013433	1.00[ASN][1000 genomes]
rs3013441	0.83[GIH][hapmap]
rs35221527	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3795820	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs4839257	0.92[GIH][hapmap]
rs6537740	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6537741	1.00[JPT][hapmap]
rs6537742	0.82[JPT][hapmap]
rs6537747	0.92[GIH][hapmap]
rs6658555	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs6668533	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs6671645	0.92[GIH][hapmap]
rs6681371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs7415988	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2932537	ST7L	cis	multi-tissue	Pritchard
rs2932537	CAPZA1	cis	brain	seeQTL
rs2932537	CAPZA1	trans	brain	seeQTL
rs2932537	DENND2C	cis	parietal	SCAN
rs2932537	CTTNBP2NL	cis	parietal	SCAN
rs2932537	EPS8L3	cis	cerebellum	SCAN
rs2932537	MOV10	cis	parietal	SCAN
rs2932537	HBXIP	cis	parietal	SCAN
rs2932537	SORT1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113218400-113230400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:113218400-113234200	Weak transcription	Aorta	Aorta
3	chr1:113218600-113232200	Weak transcription	Ovary	ovary
4	chr1:113218600-113235000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:113218600-113235400	Weak transcription	HSMM	muscle
6	chr1:113218600-113240800	Weak transcription	Right Atrium	heart
7	chr1:113218800-113230400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:113218800-113230600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:113218800-113232200	Weak transcription	Colonic Mucosa	Colon
10	chr1:113218800-113232400	Weak transcription	Brain Substantia Nigra	brain
11	chr1:113218800-113234200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:113219000-113230600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:113219000-113231400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:113219000-113232000	Weak transcription	Hela-S3	cervix
15	chr1:113219000-113232200	Weak transcription	Small Intestine	intestine
16	chr1:113219000-113232400	Weak transcription	Brain Anterior Caudate	brain
17	chr1:113219000-113234400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:113219000-113235400	Weak transcription	A549	lung
19	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
20	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
21	chr1:113219200-113230800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:113219200-113230800	Weak transcription	NHLF	lung
23	chr1:113219200-113232200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:113219200-113232400	Weak transcription	HUVEC	blood vessel
25	chr1:113219400-113230400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:113219400-113230400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:113219400-113230600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:113219400-113231400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:113219400-113232600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:113219400-113233200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:113219600-113230600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr1:113219600-113230600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:113219600-113230600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:113219600-113231000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:113219600-113232000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:113219600-113232200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:113219600-113232600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:113219800-113231000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:113220000-113233000	Weak transcription	Primary B cells from cord blood	blood
40	chr1:113220000-113234400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:113220200-113231400	Weak transcription	Thymus	Thymus
42	chr1:113220200-113231600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:113220600-113231000	Weak transcription	Fetal Lung	lung
44	chr1:113220800-113232200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:113221200-113232200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:113221400-113230400	Weak transcription	HepG2	liver
47	chr1:113221400-113230600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:113222000-113243000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:113222200-113234200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:113222800-113230600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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