Variant report

Variant	rs7644501
Chromosome Location	chr3:179045759-179045760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179040612..179043524-chr3:179043815..179047485,6	K562	blood:
2	chr3:179039368..179041573-chr3:179044284..179046543,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1061751	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10937003	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11539416	0.84[ASN][1000 genomes]
rs11714246	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714353	0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11715130	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715227	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs11716462	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720405	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12632708	0.85[ASN][1000 genomes]
rs12634184	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs13327561	0.85[JPT][hapmap]
rs16848314	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2111278	0.95[CHD][hapmap];0.95[JPT][hapmap]
rs2287212	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2287311	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs3806687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55916170	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62410442	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410443	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410445	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6794532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73172210	0.83[ASN][1000 genomes]
rs7610174	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642257	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS 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 target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7644501	MFN1	cis	cerebellum	SCAN
rs7644501	GNB4	cis	parietal	SCAN
rs7644501	GNB4	cis	cerebellum	SCAN
rs7644501	MFN1	cis	parietal	SCAN
rs7644501	ZNF639	cis	parietal	SCAN
rs7644501	LAMP3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179041800-179046600	Weak transcription	Gastric	stomach
2	chr3:179041800-179046600	Weak transcription	Small Intestine	intestine
3	chr3:179041800-179048000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:179042000-179046200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:179042400-179051800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:179042600-179046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:179042600-179046600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:179042600-179046600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:179042600-179046600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:179042600-179046600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:179042600-179048000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:179042600-179048000	Weak transcription	Colonic Mucosa	Colon
13	chr3:179042600-179054000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:179042800-179045800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:179042800-179045800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:179042800-179045800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:179042800-179046400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:179042800-179046600	Weak transcription	Brain Angular Gyrus	brain
19	chr3:179042800-179046600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:179042800-179046600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:179042800-179046600	Weak transcription	Thymus	Thymus
22	chr3:179042800-179046600	Weak transcription	HSMMtube	muscle
23	chr3:179042800-179047600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:179043000-179045800	Weak transcription	Adipose Nuclei	Adipose
25	chr3:179043000-179046600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:179043000-179046600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:179043000-179046600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:179043000-179046800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:179043000-179046800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:179043000-179048000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:179043000-179048000	Weak transcription	Esophagus	oesophagus
32	chr3:179043000-179050000	Weak transcription	Aorta	Aorta
33	chr3:179043000-179050000	Weak transcription	Psoas Muscle	Psoas
34	chr3:179043000-179054800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:179043000-179054800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:179043000-179055600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:179043200-179046000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:179043200-179046200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:179043200-179046400	Weak transcription	Primary B cells from cord blood	blood
40	chr3:179043200-179046400	Weak transcription	Fetal Brain Female	brain
41	chr3:179043200-179046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:179043200-179046600	Weak transcription	Lung	lung
43	chr3:179043200-179046600	Weak transcription	Ovary	ovary
44	chr3:179043200-179046600	Weak transcription	Pancreas	Pancrea
45	chr3:179043200-179046600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:179043200-179046600	Weak transcription	Spleen	Spleen
47	chr3:179043200-179046800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:179043200-179046800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:179043200-179048600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:179043200-179051400	Weak transcription	Fetal Heart	heart

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