Variant report

Variant	rs10195619
Chromosome Location	chr2:112765562-112765563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112763171..112764679-chr2:112764744..112767123,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10169022	0.81[CEU][hapmap]
rs10176769	0.81[CEU][hapmap]
rs10192602	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192728	0.81[CEU][hapmap]
rs10496439	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10864895	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122970	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11673729	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11674226	0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11674883	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11674891	0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11675946	0.92[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs11678522	0.81[ASN][1000 genomes]
rs11679801	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11680463	0.81[ASN][1000 genomes]
rs11681063	1.00[ASN][1000 genomes]
rs11682629	0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs11683694	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11684321	0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs11685190	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs11686647	0.84[ASN][1000 genomes]
rs11687451	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11692445	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13003919	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs13006203	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13013340	0.87[ASN][1000 genomes]
rs13013943	0.87[ASN][1000 genomes]
rs13020304	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs13020353	0.90[ASN][1000 genomes]
rs13025651	0.81[ASN][1000 genomes]
rs13027171	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13033393	0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1554216	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs17174697	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs17779482	0.92[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1967530	0.81[ASN][1000 genomes]
rs2271701	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs34527376	1.00[ASN][1000 genomes]
rs34705448	1.00[ASN][1000 genomes]
rs34875611	1.00[ASN][1000 genomes]
rs34928784	0.81[ASN][1000 genomes]
rs34974369	0.84[ASN][1000 genomes]
rs34983493	0.81[ASN][1000 genomes]
rs35189728	0.90[ASN][1000 genomes]
rs35379879	0.90[ASN][1000 genomes]
rs35382200	0.81[ASN][1000 genomes]
rs35471545	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761699	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3811633	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs3811634	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs4264571	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4441478	0.80[ASN][1000 genomes]
rs4848229	0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4848238	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs4848241	1.00[ASN][1000 genomes]
rs4848861	0.92[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4848874	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4848899	0.90[ASN][1000 genomes]
rs4848979	0.81[CEU][hapmap]
rs56361454	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6541942	0.81[ASN][1000 genomes]
rs6722814	0.81[CEU][hapmap]
rs6731215	0.84[ASN][1000 genomes]
rs6736093	0.92[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6743523	0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6754526	1.00[ASN][1000 genomes]
rs6755101	0.81[ASN][1000 genomes]
rs71414616	0.87[ASN][1000 genomes]
rs7349221	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7370418	0.87[ASN][1000 genomes]
rs74182850	0.84[ASN][1000 genomes]
rs7422195	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7578435	0.90[ASN][1000 genomes]
rs7595212	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7604403	0.92[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs870761	0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs870763	0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS 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	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv999746	chr2:112691270-112796083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1003129	chr2:112691270-112816694	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv2760607	chr2:112691282-112803423	Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv431491	chr2:112699350-112793981	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv515698	chr2:112699350-112795908	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv933392	chr2:112747230-112792349	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10195619	EDAR	cis	cerebellum	SCAN
rs10195619	TMEM87B	cis	multi-tissue	Pritchard
rs10195619	RANBP2	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112713200-112790600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:112718400-112776400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:112723400-112789200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:112726200-112767600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:112730800-112770400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:112732600-112771200	Strong transcription	Liver	Liver
7	chr2:112733200-112789200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:112740400-112768400	Weak transcription	Colonic Mucosa	Colon
9	chr2:112741400-112777000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:112741400-112777000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:112742000-112776800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:112742400-112765800	Weak transcription	Placenta	Placenta
13	chr2:112744200-112777000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:112744200-112777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:112744400-112767800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:112744600-112774000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:112753000-112784000	Weak transcription	Fetal Lung	lung
18	chr2:112753600-112771600	Strong transcription	HepG2	liver
19	chr2:112754200-112767800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:112754400-112767800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:112755400-112789200	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:112755600-112767600	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:112756200-112766200	Weak transcription	Brain Anterior Caudate	brain
24	chr2:112756200-112767600	Weak transcription	Brain Substantia Nigra	brain
25	chr2:112756200-112768200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:112757800-112766200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:112757800-112767600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:112758200-112765600	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:112758200-112765600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:112758200-112765800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:112758200-112789600	Weak transcription	Fetal Kidney	kidney
32	chr2:112758400-112766600	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:112759200-112766400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:112759200-112777000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:112759400-112768000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:112761600-112765800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:112761600-112767600	Weak transcription	Spleen	Spleen
38	chr2:112761800-112765800	Weak transcription	Aorta	Aorta
39	chr2:112761800-112767400	Weak transcription	Adipose Nuclei	Adipose
40	chr2:112761800-112767800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:112761800-112767800	Weak transcription	Gastric	stomach
42	chr2:112761800-112767800	Weak transcription	Lung	lung
43	chr2:112761800-112784000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:112762000-112765800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:112762000-112765800	Weak transcription	Left Ventricle	heart
46	chr2:112762000-112767600	Weak transcription	Pancreas	Pancrea
47	chr2:112762000-112777000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:112762200-112765800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:112762200-112765800	Weak transcription	HUVEC	blood vessel
50	chr2:112762200-112767600	Weak transcription	Ovary	ovary

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