Variant report

Variant	rs7650230
Chromosome Location	chr3:93694359-93694360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr3:93694320-93694367	K562	blood:	n/a	n/a
2	ZMIZ1	chr3:93694316-93694367	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:93691441..93695260-chr3:93696863..93699033,5	MCF-7	breast:
2	chr3:93690937..93695495-chr3:93697759..93704969,13	K562	blood:

Variant related genes	Relation type
RNU6-511P	TF binding region
PROS1	TF binding region
ARL13B	TF binding region
ENSG00000169379	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12488200	0.94[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs4133534	0.91[EUR][1000 genomes]
rs4414894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4434178	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4535269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4857173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs4857343	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5013930	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441601	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771653	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]
rs6773487	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6786905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6803590	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8178583	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290469	0.81[EUR][1000 genomes]
rs9681204	0.82[EUR][1000 genomes]
rs9713029	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs9713061	0.82[EUR][1000 genomes]
rs9821535	0.80[EUR][1000 genomes]
rs9843295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002292	chr3:93519466-93736214	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS 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	14 gene(s)	inside rSNPs	n/a
2	nsv998051	chr3:93519466-93740680	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
3	nsv1005328	chr3:93519466-93743921	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv533358	chr3:93575289-93745823	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	n/a
11	nsv916541	chr3:93575289-93758589	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
12	esv1803747	chr3:93602038-93759079	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
13	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
14	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
15	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
16	nsv1003434	chr3:93654100-93740824	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
17	nsv536647	chr3:93654100-93740824	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
18	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
19	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
20	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7650230	ARL6	cis	cerebellum	SCAN
rs7650230	TMX4	trans	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93693000-93698400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:93693000-93698400	Weak transcription	Placenta	Placenta
3	chr3:93693000-93698400	Weak transcription	Thymus	Thymus
4	chr3:93693200-93696600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:93693200-93696600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:93693200-93698200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:93693200-93698200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:93693200-93698200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:93693200-93698200	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:93693200-93698200	Weak transcription	A549	lung
11	chr3:93693200-93698200	Weak transcription	Dnd41	blood
12	chr3:93693200-93698200	Weak transcription	NHDF-Ad	bronchial
13	chr3:93693200-93698400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:93693200-93698400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:93693200-93698400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:93693200-93698400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:93693200-93698400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:93693200-93698400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:93693200-93698400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:93693200-93698400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:93693200-93698400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:93693200-93698400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:93693200-93698400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:93693200-93698400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:93693200-93698400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:93693200-93698400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:93693200-93698400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:93693200-93698400	Weak transcription	Adipose Nuclei	Adipose
29	chr3:93693200-93698400	Weak transcription	Liver	Liver
30	chr3:93693200-93698400	Weak transcription	Brain Germinal Matrix	brain
31	chr3:93693200-93698400	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:93693200-93698400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:93693200-93698400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:93693200-93698400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:93693200-93698400	Weak transcription	Fetal Brain Male	brain
36	chr3:93693200-93698400	Weak transcription	Fetal Heart	heart
37	chr3:93693200-93698400	Weak transcription	Fetal Lung	lung
38	chr3:93693200-93698400	Weak transcription	Fetal Thymus	thymus
39	chr3:93693200-93698400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:93693200-93698400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:93693200-93698400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:93693200-93698400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:93693200-93698400	Weak transcription	Stomach Mucosa	stomach
44	chr3:93693200-93698400	Weak transcription	Hela-S3	cervix
45	chr3:93693200-93698400	Weak transcription	HMEC	breast
46	chr3:93693200-93698400	Weak transcription	HSMMtube	muscle
47	chr3:93693200-93698400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:93693200-93698400	Weak transcription	NHEK	skin
49	chr3:93693200-93698600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:93693200-93698800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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