Variant report

Variant	rs11680916
Chromosome Location	chr2:48585158-48585159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48578562..48582388-chr2:48582784..48586939,6	K562	blood:
2	chr2:48578681..48582388-chr2:48582784..48586647,4	K562	blood:
3	chr2:48583541..48585248-chr2:48599640..48601828,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10153773	0.91[JPT][hapmap]
rs10169629	0.92[ASN][1000 genomes]
rs10186237	0.82[JPT][hapmap]
rs10199431	0.91[JPT][hapmap]
rs10208627	0.85[ASN][1000 genomes]
rs10454133	0.82[JPT][hapmap]
rs10454134	0.83[JPT][hapmap]
rs10495951	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10495952	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11676036	0.80[EUR][1000 genomes]
rs11676168	0.95[JPT][hapmap]
rs11679523	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680719	0.87[JPT][hapmap]
rs11682044	0.86[JPT][hapmap]
rs11682633	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11683099	0.94[ASN][1000 genomes]
rs11683639	0.86[JPT][hapmap]
rs11684517	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11685861	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11686007	0.86[ASN][1000 genomes]
rs11687708	0.81[ASN][1000 genomes]
rs11688481	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11689622	0.86[JPT][hapmap]
rs11689645	0.92[ASN][1000 genomes]
rs11690690	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11690748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11690845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12052754	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12105983	0.85[ASN][1000 genomes]
rs12328506	0.93[ASN][1000 genomes]
rs13388291	0.90[JPT][hapmap]
rs13398791	0.93[ASN][1000 genomes]
rs13401749	0.86[JPT][hapmap]
rs13432998	0.91[JPT][hapmap]
rs17037289	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17037298	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17855177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[ASN][1000 genomes]
rs4316980	0.86[JPT][hapmap]
rs4344965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4411759	0.91[JPT][hapmap]
rs4438532	0.83[JPT][hapmap]
rs4547570	0.93[ASN][1000 genomes]
rs4606978	0.82[JPT][hapmap]
rs4641990	0.95[JPT][hapmap]
rs55660911	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55744465	0.90[ASN][1000 genomes]
rs55761545	0.90[ASN][1000 genomes]
rs55788229	0.81[ASN][1000 genomes]
rs56156294	0.90[ASN][1000 genomes]
rs56163539	0.89[ASN][1000 genomes]
rs56365822	0.82[ASN][1000 genomes]
rs56391806	0.90[ASN][1000 genomes]
rs57131168	0.85[ASN][1000 genomes]
rs57537506	0.96[ASN][1000 genomes]
rs57893565	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs58012056	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs58978223	0.81[ASN][1000 genomes]
rs59045263	0.85[ASN][1000 genomes]
rs59697023	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60042255	0.82[ASN][1000 genomes]
rs60815228	0.83[ASN][1000 genomes]
rs60825643	0.92[ASN][1000 genomes]
rs61303367	0.82[ASN][1000 genomes]
rs62137001	0.89[AFR][1000 genomes]
rs62137015	0.98[ASN][1000 genomes]
rs62137019	0.83[ASN][1000 genomes]
rs62137021	0.82[ASN][1000 genomes]
rs6545027	0.87[JPT][hapmap]
rs6545030	0.95[JPT][hapmap]
rs6545036	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs66705539	0.84[ASN][1000 genomes]
rs6705802	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6712029	0.95[JPT][hapmap]
rs6718068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6722246	0.99[ASN][1000 genomes]
rs6735288	0.85[ASN][1000 genomes]
rs6743757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6745580	0.96[ASN][1000 genomes]
rs6749773	0.82[ASN][1000 genomes]
rs6756596	0.96[ASN][1000 genomes]
rs72818488	0.84[ASN][1000 genomes]
rs72818491	0.82[ASN][1000 genomes]
rs72818494	0.83[ASN][1000 genomes]
rs72818502	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72820403	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820404	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72820409	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820411	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820415	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820416	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820418	0.94[ASN][1000 genomes]
rs72820420	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820422	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72820423	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820424	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820427	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs72820433	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820436	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72820437	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820439	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820441	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72820445	0.99[ASN][1000 genomes]
rs72820454	0.82[ASN][1000 genomes]
rs7559431	0.94[ASN][1000 genomes]
rs7562069	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7562816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7566239	0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7568574	0.83[ASN][1000 genomes]
rs7573316	0.99[ASN][1000 genomes]
rs7576964	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7577237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7579932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7600794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7606104	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11680916	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
2	chr2:48572200-48597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:48573600-48604000	Weak transcription	Ovary	ovary
4	chr2:48574200-48602000	Weak transcription	Gastric	stomach
5	chr2:48574600-48602000	Weak transcription	Small Intestine	intestine
6	chr2:48574800-48589600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:48574800-48589600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:48576200-48597000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:48576200-48602000	Weak transcription	Lung	lung
10	chr2:48576400-48590000	Weak transcription	Placenta	Placenta
11	chr2:48576600-48595600	Weak transcription	Fetal Brain Female	brain
12	chr2:48576600-48602000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:48577600-48589600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:48577600-48589600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:48577800-48592400	Weak transcription	Right Atrium	heart
16	chr2:48577800-48602000	Weak transcription	Fetal Kidney	kidney
17	chr2:48577800-48603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:48578600-48591000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:48578600-48604800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:48578800-48589000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:48578800-48589600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:48579000-48586000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:48579000-48589400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:48579000-48595000	Weak transcription	Esophagus	oesophagus
25	chr2:48579000-48595000	Weak transcription	Fetal Stomach	stomach
26	chr2:48579200-48593000	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:48579200-48595400	Weak transcription	Fetal Intestine Large	intestine
28	chr2:48579400-48589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:48580400-48585600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:48580400-48595200	Weak transcription	HSMMtube	muscle
31	chr2:48580600-48585200	Weak transcription	A549	lung
32	chr2:48580600-48587600	Weak transcription	HSMM	muscle
33	chr2:48580600-48588200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:48580600-48601800	Weak transcription	Hela-S3	cervix
35	chr2:48580800-48589000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:48580800-48591800	Weak transcription	NH-A	brain
37	chr2:48580800-48599800	Weak transcription	NHEK	skin
38	chr2:48580800-48602000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:48580800-48602000	Weak transcription	Osteobl	bone
40	chr2:48580800-48604000	Weak transcription	Aorta	Aorta
41	chr2:48581000-48593400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:48581200-48590800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:48581400-48589400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:48581400-48589400	Weak transcription	Brain Anterior Caudate	brain
45	chr2:48581400-48589400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:48581400-48589600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:48581400-48589600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:48581400-48589600	Weak transcription	NHLF	lung
49	chr2:48581400-48589800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:48581400-48589800	Weak transcription	Rectal Mucosa Donor 29	rectum

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