Variant report

Variant	rs2305705
Chromosome Location	chr15:72447621-72447622
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	chr15:72445875..72448342-chr15:72461656..72463455,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRAMD2-1	chr15:72447524-72447800	ENSG00000260173.1

Variant related genes	Relation type
ENSG00000175318	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11072341	0.90[ASN][1000 genomes]
rs11072343	0.96[ASN][1000 genomes]
rs11072344	0.93[ASN][1000 genomes]
rs11072355	1.00[CEU][hapmap]
rs1120002	0.90[ASN][1000 genomes]
rs12437582	0.80[ASN][1000 genomes]
rs12438532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12439689	0.94[ASN][1000 genomes]
rs12440204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12440299	0.94[ASN][1000 genomes]
rs12440435	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12440927	1.00[CEU][hapmap]
rs12441246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12441470	0.90[ASN][1000 genomes]
rs12441567	0.90[ASN][1000 genomes]
rs12441622	0.90[ASN][1000 genomes]
rs12442680	1.00[ASN][1000 genomes]
rs12443127	0.90[ASN][1000 genomes]
rs12592615	0.98[ASN][1000 genomes]
rs12592858	0.96[ASN][1000 genomes]
rs12592932	0.96[ASN][1000 genomes]
rs12592969	0.98[ASN][1000 genomes]
rs12593082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12593857	0.90[ASN][1000 genomes]
rs12593946	0.90[ASN][1000 genomes]
rs12911449	1.00[CEU][hapmap]
rs1426168	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1545825	0.86[ASN][1000 genomes]
rs16953770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16956539	0.90[ASN][1000 genomes]
rs16956599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16956602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16956723	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1871834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2288256	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs28397923	1.00[ASN][1000 genomes]
rs28639924	0.90[ASN][1000 genomes]
rs28653163	0.90[ASN][1000 genomes]
rs28701834	0.90[ASN][1000 genomes]
rs2912226	1.00[CEU][hapmap]
rs2912229	1.00[CEU][hapmap]
rs2929514	0.80[ASN][1000 genomes]
rs2929515	0.80[ASN][1000 genomes]
rs2929521	0.86[ASN][1000 genomes]
rs2929522	0.86[ASN][1000 genomes]
rs2929524	0.80[ASN][1000 genomes]
rs2929530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2929531	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2929533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2957369	0.86[ASN][1000 genomes]
rs2957729	0.80[ASN][1000 genomes]
rs2957730	0.80[ASN][1000 genomes]
rs2957741	0.86[ASN][1000 genomes]
rs2957747	0.86[ASN][1000 genomes]
rs2957749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2959915	1.00[CEU][hapmap]
rs34625473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs35773391	0.90[ASN][1000 genomes]
rs3803388	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs3809505	0.98[ASN][1000 genomes]
rs3825869	0.86[ASN][1000 genomes]
rs4442765	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4511484	0.86[ASN][1000 genomes]
rs6495000	1.00[CEU][hapmap]
rs7161909	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7164646	0.90[ASN][1000 genomes]
rs7165735	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7171446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7175907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7178613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8026894	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8029218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8032957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8039245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8192381	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9920148	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats 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	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription 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	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72445800-72448000	Enhancers	Fetal Lung	lung
2	chr15:72446400-72447800	Enhancers	Lung	lung
3	chr15:72446400-72448200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:72446600-72447800	Enhancers	Fetal Brain Male	brain
5	chr15:72447000-72447800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr15:72447200-72447800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr15:72447200-72447800	Enhancers	HUVEC	blood vessel
8	chr15:72447200-72448800	Flanking Active TSS	A549	lung
9	chr15:72447400-72447800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:72447400-72447800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:72447400-72447800	Enhancers	Aorta	Aorta
12	chr15:72447400-72447800	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr15:72447400-72447800	Enhancers	Ovary	ovary
14	chr15:72447400-72447800	Flanking Active TSS	Rectal Smooth Muscle	rectum
15	chr15:72447400-72447800	Flanking Active TSS	Stomach Mucosa	stomach
16	chr15:72447400-72447800	Enhancers	Hela-S3	cervix
17	chr15:72447400-72447800	Flanking Bivalent TSS/Enh	HepG2	liver
18	chr15:72447400-72447800	Enhancers	HSMM	muscle
19	chr15:72447400-72447800	Enhancers	NHLF	lung
20	chr15:72447400-72448000	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr15:72447400-72448000	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr15:72447400-72448000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr15:72447400-72448000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:72447400-72448000	Enhancers	GM12878-XiMat	blood
25	chr15:72447400-72448200	Active TSS	Pancreas	Pancrea
26	chr15:72447400-72448600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:72447400-72448600	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr15:72447400-72448600	Flanking Active TSS	Liver	Liver
29	chr15:72447400-72448600	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr15:72447400-72448600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr15:72447400-72448800	Flanking Active TSS	HMEC	breast
32	chr15:72447400-72449000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:72447400-72449000	Active TSS	Colonic Mucosa	Colon
34	chr15:72447400-72449000	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr15:72447400-72449200	Active TSS	Fetal Kidney	kidney
36	chr15:72447600-72447800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr15:72447600-72447800	Enhancers	Fetal Intestine Large	intestine
38	chr15:72447600-72447800	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr15:72447600-72447800	Flanking Active TSS	Left Ventricle	heart
40	chr15:72447600-72447800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr15:72447600-72447800	Active TSS	Spleen	Spleen
42	chr15:72447600-72448000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:72447600-72448000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:72447600-72448000	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr15:72447600-72448000	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr15:72447600-72448000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr15:72447600-72448000	Flanking Active TSS	Esophagus	oesophagus
48	chr15:72447600-72448000	Flanking Active TSS	Right Ventricle	heart
49	chr15:72447600-72448200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
50	chr15:72447600-72448200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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