Variant report

Variant	rs7635444
Chromosome Location	chr3:141795573-141795574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13322825	0.85[ASN][1000 genomes]
rs1704985	0.81[ASN][1000 genomes]
rs1705607	0.81[ASN][1000 genomes]
rs1912719	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs347679	0.91[ASN][1000 genomes]
rs347685	0.81[ASN][1000 genomes]
rs347686	0.81[ASN][1000 genomes]
rs347687	0.96[ASN][1000 genomes]
rs347692	0.89[ASN][1000 genomes]
rs4683421	0.84[ASN][1000 genomes]
rs5028811	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs58573615	0.90[ASN][1000 genomes]
rs62284572	0.80[ASN][1000 genomes]
rs62284574	0.82[ASN][1000 genomes]
rs62284579	0.83[EUR][1000 genomes]
rs6773343	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs6789998	0.93[ASN][1000 genomes]
rs6797841	0.84[ASN][1000 genomes]
rs6798162	0.82[ASN][1000 genomes]
rs6801547	0.89[ASN][1000 genomes]
rs73232681	0.83[ASN][1000 genomes]
rs7652340	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9837768	0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9869592	0.84[ASN][1000 genomes]
rs9877817	0.90[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv2757013	chr3:141756541-142094631	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1002123	chr3:141789746-141956778	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv536733	chr3:141789746-141956778	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1004784	chr3:141789746-142070290	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7635444	RNF149	trans	cerebellum	SCAN
rs7635444	MOSC1	trans	cerebellum	SCAN
rs7635444	PLS1	cis	cerebellum	SCAN
rs7635444	CHST2	cis	cerebellum	SCAN
rs7635444	TTC5	trans	brain	seeQTL
rs7635444	PLSCR1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141760600-141800800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:141761000-141807800	Weak transcription	Fetal Lung	lung
3	chr3:141761800-141819600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:141763000-141820000	Weak transcription	Pancreas	Pancrea
5	chr3:141763000-141824200	Weak transcription	Aorta	Aorta
6	chr3:141764000-141825600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:141765000-141818800	Weak transcription	Primary B cells from cord blood	blood
8	chr3:141767000-141798000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:141767600-141807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:141770400-141795800	Weak transcription	Fetal Stomach	stomach
11	chr3:141774400-141798800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:141776000-141805400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:141776400-141795800	Weak transcription	Ovary	ovary
14	chr3:141780600-141796400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:141780800-141796400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:141783000-141795800	Weak transcription	Psoas Muscle	Psoas
17	chr3:141784000-141796000	Weak transcription	Lung	lung
18	chr3:141784600-141796000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:141785200-141796600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:141785800-141796200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:141789600-141805000	Weak transcription	HepG2	liver
22	chr3:141790000-141795800	Weak transcription	Colonic Mucosa	Colon
23	chr3:141790200-141796000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:141790400-141801600	Weak transcription	Brain Anterior Caudate	brain
25	chr3:141791600-141796000	Weak transcription	Dnd41	blood
26	chr3:141792200-141795600	Weak transcription	Fetal Intestine Large	intestine
27	chr3:141792200-141795800	Weak transcription	Fetal Intestine Small	intestine
28	chr3:141792200-141795800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:141792200-141796000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:141792200-141796000	Weak transcription	Small Intestine	intestine
31	chr3:141792600-141795800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:141792800-141796600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:141792800-141800800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:141793400-141795800	Weak transcription	Thymus	Thymus
35	chr3:141794200-141795800	Weak transcription	Adipose Nuclei	Adipose
36	chr3:141794200-141796200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:141794400-141795600	Weak transcription	Fetal Thymus	thymus
38	chr3:141794400-141798600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:141794600-141798800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:141795000-141806000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:141795200-141799200	Weak transcription	Fetal Brain Female	brain
42	chr3:141795400-141835800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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