Variant report

Variant	rs352140
Chromosome Location	chr3:52256697-52256698
allele	C/T
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	chr3:52255532..52258795-chr3:52273134..52275262,3	K562	blood:
2	chr3:52255588..52257621-chr3:52273304..52275120,2	MCF-7	breast:
3	chr3:52252686..52254368-chr3:52255017..52257064,2	K562	blood:
4	chr3:52255294..52257505-chr3:52260666..52263088,3	K562	blood:
5	chr3:52254877..52257716-chr3:52310306..52313604,3	MCF-7	breast:
6	chr3:52224275..52227049-chr3:52256211..52258351,2	K562	blood:
7	chr3:52254575..52260127-chr3:52268899..52275262,6	K562	blood:
8	chr3:52253477..52257891-chr3:52262845..52266465,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000247596	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000173366	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs104903	0.94[ASN][1000 genomes]
rs1060330	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11712164	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs11717383	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs164640	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs181274	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs187084	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs352139	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352158	0.81[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs352161	0.86[ASN][1000 genomes]
rs352162	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352163	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352165	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs352166	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs352167	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs352168	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs352169	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs352170	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs352171	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap]
rs353551	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs411457	0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs524986	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs610060	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs614288	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6445358	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6802320	0.90[ASN][1000 genomes]
rs730050	0.82[JPT][hapmap]
rs7614727	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7622851	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv482084	chr3:52255098-52260179	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs352140	DNAH1	cis	cerebellum	SCAN
rs352140	SEMA3G	cis	parietal	SCAN
rs352140	SEMA3G	cis	cerebellum	SCAN
rs352140	GLT8D1	cis	lymphoblastoid	seeQTL
rs352140	NEK4	cis	cerebellum	SCAN
rs352140	RBM6	cis	cerebellum	SCAN
rs352140	NEK4	cis	parietal	SCAN
rs352140	NT5DC2	cis	lymphoblastoid	seeQTL
rs352140	SPCS1	cis	parietal	SCAN
rs352140	GNL3	cis	cerebellum	SCAN
rs352140	ITIH4	cis	parietal	SCAN
rs352140	GNL3	cis	parietal	SCAN
rs352140	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247200-52263000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:52249600-52263400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:52249800-52262400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52249800-52262400	Weak transcription	Aorta	Aorta
6	chr3:52250000-52256800	Enhancers	Fetal Muscle Leg	muscle
7	chr3:52250000-52261400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:52250000-52261800	Weak transcription	Brain Germinal Matrix	brain
9	chr3:52250000-52262200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:52250000-52262600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:52250200-52257800	Enhancers	Fetal Muscle Trunk	muscle
12	chr3:52250200-52262800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:52250600-52257000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:52250600-52257600	Genic enhancers	Primary B cells from cord blood	blood
15	chr3:52250600-52258200	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr3:52251000-52261800	Weak transcription	Fetal Brain Female	brain
17	chr3:52251000-52266600	Weak transcription	Fetal Brain Male	brain
18	chr3:52251200-52262200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:52251400-52262000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:52251400-52263200	Weak transcription	A549	lung
21	chr3:52251600-52259800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:52251600-52261600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:52251600-52261800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:52251600-52262400	Weak transcription	NHLF	lung
25	chr3:52251600-52262400	Weak transcription	Osteobl	bone
26	chr3:52251600-52262800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:52251600-52262800	Weak transcription	NHDF-Ad	bronchial
28	chr3:52251600-52263600	Weak transcription	HSMM	muscle
29	chr3:52251600-52264200	Weak transcription	HSMMtube	muscle
30	chr3:52251600-52266600	Weak transcription	Psoas Muscle	Psoas
31	chr3:52252200-52261400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:52252200-52261800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:52253000-52259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:52253000-52262000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:52253000-52262800	Weak transcription	Small Intestine	intestine
36	chr3:52253200-52256800	Enhancers	Adipose Nuclei	Adipose
37	chr3:52253200-52261800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:52253200-52263000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:52253200-52269600	Weak transcription	Fetal Kidney	kidney
40	chr3:52253400-52262400	Weak transcription	NH-A	brain
41	chr3:52253400-52263400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:52253400-52264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:52253600-52259800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:52253800-52263200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:52254000-52263000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:52254400-52256800	Enhancers	Right Ventricle	heart
47	chr3:52254400-52257000	Enhancers	Duodenum Mucosa	Duodenum
48	chr3:52254600-52256800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr3:52254800-52256800	Enhancers	Esophagus	oesophagus
50	chr3:52254800-52258400	Genic enhancers	Spleen	Spleen

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