Variant report

Variant	rs6771653
Chromosome Location	chr3:93830606-93830607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs4414894	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap]
rs4857173	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4857343	0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap]
rs5013930	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6773487	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6786905	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6803590	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap]
rs7650230	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap]
rs9821535	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9843295	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9848659	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
8	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
9	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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	19 gene(s)	inside rSNPs	n/a
10	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers 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	11 gene(s)	inside rSNPs	diseases
14	nsv877163	chr3:93795972-94047775	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6771653	TMX4	trans	cerebellum	SCAN
rs6771653	ARL6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93782800-93848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:93782800-93849400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:93783200-93851600	Weak transcription	HMEC	breast
4	chr3:93783400-93833000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:93783600-93837800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:93785600-93834400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:93786200-93834600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:93786400-93830800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:93786800-93849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:93791400-93841200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:93792200-93833200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:93795600-93847000	Weak transcription	Osteobl	bone
13	chr3:93796000-93857800	Weak transcription	Fetal Brain Male	brain
14	chr3:93799000-93851600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:93800000-93830800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:93800200-93851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:93802200-93830800	Weak transcription	Fetal Kidney	kidney
18	chr3:93802400-93849600	Weak transcription	Stomach Mucosa	stomach
19	chr3:93802600-93851800	Weak transcription	Small Intestine	intestine
20	chr3:93802800-93830800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:93803400-93835800	Weak transcription	Psoas Muscle	Psoas
22	chr3:93804400-93834600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:93804800-93833000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:93806400-93834800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:93808400-93849600	Weak transcription	Fetal Heart	heart
26	chr3:93808600-93830800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:93811400-93832800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:93812400-93852200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:93814200-93831400	Weak transcription	A549	lung
30	chr3:93814600-93845200	Weak transcription	Esophagus	oesophagus
31	chr3:93814600-93847000	Weak transcription	Spleen	Spleen
32	chr3:93814600-93849400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:93814600-93849400	Weak transcription	Right Ventricle	heart
34	chr3:93814600-93849600	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:93814600-93849800	Weak transcription	Colonic Mucosa	Colon
36	chr3:93814800-93845200	Weak transcription	Gastric	stomach
37	chr3:93814800-93857800	Weak transcription	Pancreas	Pancrea
38	chr3:93815400-93834200	Weak transcription	Brain Anterior Caudate	brain
39	chr3:93815600-93848400	Weak transcription	Placenta	Placenta
40	chr3:93815800-93832800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:93816600-93834600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:93817200-93844800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:93817400-93833000	Weak transcription	NHDF-Ad	bronchial
44	chr3:93817400-93849600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:93817600-93837200	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:93817600-93847000	Weak transcription	HepG2	liver
47	chr3:93817600-93848000	Weak transcription	NH-A	brain
48	chr3:93817800-93843000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:93817800-93846000	Weak transcription	Brain Angular Gyrus	brain
50	chr3:93817800-93848000	Weak transcription	Muscle Satellite Cultured Cells	--

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