Variant report

Variant	rs7618306
Chromosome Location	chr3:156533745-156533746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:79824042..79825935-chr3:156533606..156535804,2	MCF-7	breast:
2	chr3:156426710..156429156-chr3:156532890..156534786,2	MCF-7	breast:
3	chr3:156270408..156273288-chr3:156530835..156533779,2	MCF-7	breast:
4	chr3:156531546..156534096-chr3:156793933..156795686,2	MCF-7	breast:
5	chr3:156533499..156536526-chr3:156891417..156894235,3	MCF-7	breast:
6	chr3:156400050..156402088-chr3:156531912..156534314,2	MCF-7	breast:
7	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
8	chr3:156398277..156399955-chr3:156533630..156535549,2	MCF-7	breast:
9	chr3:156497492..156500885-chr3:156532144..156534276,3	K562	blood:
10	chr3:156397478..156399872-chr3:156533478..156536173,2	MCF-7	breast:
11	chr3:156409514..156412147-chr3:156532498..156534140,2	K562	blood:
12	chr3:156532344..156534533-chr3:156884722..156886636,3	MCF-7	breast:
13	chr3:156533566..156537799-chr3:156875553..156879495,5	MCF-7	breast:
14	chr3:156256323..156258307-chr3:156531885..156534419,2	MCF-7	breast:
15	chr3:156533151..156536166-chr3:156876536..156878958,4	MCF-7	breast:
16	chr3:156389670..156395497-chr3:156530360..156537244,22	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-10	chr3:156533269-156533862	NONHSAT092868

No data

Variant related genes	Relation type
ENSG00000243176	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000262413	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11710516	0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11717138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927500	1.00[JPT][hapmap]
rs13321802	1.00[JPT][hapmap]
rs1430412	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16826858	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16826864	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16826899	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16826906	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16826948	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs171077	0.89[ASN][1000 genomes]
rs171080	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs180746	0.89[ASN][1000 genomes]
rs182936	0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2163296	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs237246	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2633815	1.00[JPT][hapmap]
rs2653817	0.84[GIH][hapmap]
rs28661978	0.84[ASN][1000 genomes]
rs2874490	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2874491	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs343992	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344023	0.89[ASN][1000 genomes]
rs344030	0.84[AMR][1000 genomes]
rs344032	0.84[ASN][1000 genomes]
rs344047	0.89[ASN][1000 genomes]
rs344048	0.89[ASN][1000 genomes]
rs344049	0.89[ASN][1000 genomes]
rs344050	0.89[ASN][1000 genomes]
rs344063	1.00[JPT][hapmap]
rs344076	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344077	0.84[ASN][1000 genomes]
rs344078	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344081	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344083	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344085	0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs344086	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344088	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344090	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344091	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344092	1.00[JPT][hapmap]
rs3796172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414683	1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4680298	0.83[CHD][hapmap]
rs4680299	0.83[CHD][hapmap]
rs4680304	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491423	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs59244547	0.84[ASN][1000 genomes]
rs6441092	0.83[CHD][hapmap]
rs6441099	1.00[JPT][hapmap]
rs6441100	1.00[JPT][hapmap]
rs6441104	1.00[JPT][hapmap]
rs6763233	1.00[JPT][hapmap]
rs6763644	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6786167	1.00[JPT][hapmap]
rs6787535	1.00[JPT][hapmap]
rs6787952	1.00[JPT][hapmap]
rs6792917	1.00[JPT][hapmap]
rs6795327	1.00[JPT][hapmap]
rs6795516	1.00[JPT][hapmap]
rs6799457	0.83[CHD][hapmap]
rs6802042	1.00[JPT][hapmap]
rs6802511	1.00[JPT][hapmap]
rs7609851	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7630909	1.00[JPT][hapmap]
rs7634472	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7635521	1.00[JPT][hapmap]
rs7650127	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs978108	0.83[CHD][hapmap]
rs9847692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858861	0.88[GIH][hapmap]
rs9861359	1.00[JPT][hapmap]
rs9878709	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7618306	SSR3	cis	parietal	SCAN
rs7618306	IQCJ	cis	parietal	SCAN
rs7618306	METAP2	trans	parietal	SCAN
rs7618306	OTOL1	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156527400-156533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:156527800-156533800	Enhancers	HMEC	breast
3	chr3:156530600-156533800	Weak transcription	Lung	lung
4	chr3:156530800-156533800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:156530800-156533800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:156530800-156533800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:156530800-156533800	Weak transcription	Left Ventricle	heart
8	chr3:156531000-156533800	Weak transcription	Right Ventricle	heart
9	chr3:156531000-156533800	Weak transcription	Small Intestine	intestine
10	chr3:156531200-156533800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:156531200-156533800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:156531200-156533800	Weak transcription	Esophagus	oesophagus
13	chr3:156531200-156533800	Weak transcription	Pancreas	Pancrea
14	chr3:156531200-156533800	Weak transcription	Psoas Muscle	Psoas
15	chr3:156531200-156533800	Weak transcription	Right Atrium	heart
16	chr3:156531200-156533800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:156531200-156533800	Weak transcription	HSMM	muscle
18	chr3:156531200-156534000	Weak transcription	Aorta	Aorta
19	chr3:156531200-156534000	Weak transcription	Gastric	stomach
20	chr3:156531200-156534200	Weak transcription	Stomach Mucosa	stomach
21	chr3:156531400-156534000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:156531400-156534600	Weak transcription	K562	blood
23	chr3:156531600-156533800	Active TSS	GM12878-XiMat	blood
24	chr3:156531800-156534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:156532400-156533800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:156532800-156533800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:156533000-156534200	Bivalent Enhancer	Fetal Brain Male	brain
28	chr3:156533200-156533800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:156533200-156533800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:156533200-156533800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr3:156533200-156534200	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr3:156533200-156535400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr3:156533200-156536200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:156533400-156533800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
35	chr3:156533400-156533800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
36	chr3:156533400-156533800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
37	chr3:156533400-156533800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr3:156533400-156533800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:156533400-156533800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:156533400-156533800	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
41	chr3:156533400-156533800	Bivalent Enhancer	Fetal Lung	lung
42	chr3:156533400-156533800	Flanking Active TSS	A549	lung
43	chr3:156533400-156533800	Flanking Active TSS	NHEK	skin
44	chr3:156533400-156533800	Enhancers	NHLF	lung
45	chr3:156533400-156534000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr3:156533400-156534000	Enhancers	Primary T cells from cord blood	blood
47	chr3:156533400-156534000	Enhancers	HepG2	liver
48	chr3:156533400-156534200	Flanking Active TSS	Liver	Liver
49	chr3:156533400-156534200	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr3:156533400-156534400	Flanking Active TSS	NHDF-Ad	bronchial

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