Variant report

Variant	rs4538631
Chromosome Location	chr5:95405343-95405344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10052503	0.82[CHB][hapmap]
rs10073752	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10073810	0.85[ASN][1000 genomes]
rs10515232	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1057963	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs11738945	0.87[JPT][hapmap]
rs11742959	0.87[JPT][hapmap]
rs11744881	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs1423269	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs17085249	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs17085333	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs17085428	0.95[CEU][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2042340	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2161318	0.82[CHB][hapmap]
rs2546199	0.82[CHB][hapmap]
rs3777162	0.82[CHB][hapmap]
rs3777163	0.82[CHB][hapmap]
rs3777165	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3777166	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3777171	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3777173	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs3777175	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3777178	0.82[CHB][hapmap]
rs3777179	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3777183	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs3777184	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3777185	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3777188	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3777189	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3777190	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3777193	0.82[JPT][hapmap]
rs3777200	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3815768	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs58666663	0.87[ASN][1000 genomes]
rs66853776	0.87[ASN][1000 genomes]
rs6861531	0.82[CHB][hapmap]
rs6865400	0.85[ASN][1000 genomes]
rs6875999	0.87[ASN][1000 genomes]
rs6881872	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6889029	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs72656691	0.83[ASN][1000 genomes]
rs72656692	0.85[ASN][1000 genomes]
rs7700895	0.82[CHB][hapmap]
rs7717348	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7717481	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7724599	0.82[CHB][hapmap]
rs9314162	0.82[CHB][hapmap];0.81[JPT][hapmap]

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	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv823146	chr5:95300912-95453557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	esv2757121	chr5:95304236-95539536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	esv34203	chr5:95310985-95452324	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv522097	chr5:95347786-95425199	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv522465	chr5:95347786-95425199	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4538631	TTC37	cis	cerebellum	SCAN
rs4538631	RIOK2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95401600-95416400	Weak transcription	Psoas Muscle	Psoas
2	chr5:95402000-95406800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:95402000-95410600	Weak transcription	Stomach Mucosa	stomach
4	chr5:95402200-95406200	Weak transcription	Colonic Mucosa	Colon
5	chr5:95402200-95406200	Weak transcription	HepG2	liver
6	chr5:95402200-95406800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:95402600-95410600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:95402600-95423800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:95404000-95406200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:95404200-95405400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:95404200-95405600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:95404200-95405600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:95404200-95406000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:95404200-95406200	Weak transcription	Placenta	Placenta
15	chr5:95404200-95406400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:95404200-95410200	Weak transcription	Pancreas	Pancrea
17	chr5:95404200-95410200	Weak transcription	Small Intestine	intestine
18	chr5:95404400-95406000	Weak transcription	A549	lung
19	chr5:95404400-95406200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:95404400-95408400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:95404400-95410200	Weak transcription	HSMM	muscle
22	chr5:95404400-95416800	Weak transcription	Aorta	Aorta
23	chr5:95404600-95410200	Weak transcription	Osteobl	bone
24	chr5:95404800-95405800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:95404800-95406000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:95404800-95406000	Weak transcription	HMEC	breast
27	chr5:95404800-95406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:95404800-95406400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:95404800-95406400	Weak transcription	NHEK	skin
30	chr5:95404800-95410200	Weak transcription	HUVEC	blood vessel
31	chr5:95404800-95411600	Weak transcription	NHDF-Ad	bronchial
32	chr5:95405000-95405400	Weak transcription	Hela-S3	cervix
33	chr5:95405000-95405400	Weak transcription	NHLF	lung
34	chr5:95405000-95406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:95405200-95408200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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