Variant report

Variant	rs3801111
Chromosome Location	chr7:38947742-38947743
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38938879..38942255-chr7:38943779..38948503,4	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10085898	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs1019065	0.98[ASN][1000 genomes]
rs10229531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242807	0.82[CHB][hapmap]
rs10243110	0.82[CHB][hapmap]
rs10244302	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10244901	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10245301	0.81[AFR][1000 genomes]
rs10245322	1.00[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]
rs10245333	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249090	0.86[ASN][1000 genomes]
rs10250120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10251632	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10252285	0.82[CHB][hapmap]
rs10262154	0.82[CHB][hapmap]
rs10266910	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269756	0.98[ASN][1000 genomes]
rs10272658	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10274968	0.81[CEU][hapmap];0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs10279181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279367	0.82[CHB][hapmap]
rs10279990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281589	0.82[CHB][hapmap]
rs10281823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951576	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs10951578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773094	0.82[CHB][hapmap]
rs11980197	0.98[ASN][1000 genomes]
rs11980627	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs11983390	0.98[ASN][1000 genomes]
rs12533017	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs12533808	0.86[ASN][1000 genomes]
rs12535711	0.96[ASN][1000 genomes]
rs12672018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228087	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs1473138	0.86[ASN][1000 genomes]
rs1473139	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs17618395	0.84[ASN][1000 genomes]
rs17619021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680408	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs17680879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008199	0.92[ASN][1000 genomes]
rs2009277	0.98[ASN][1000 genomes]
rs2067683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072247	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072248	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs2074853	0.87[ASN][1000 genomes]
rs2159018	0.82[CHB][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2189853	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2286078	0.82[CHB][hapmap]
rs2286107	0.82[CHB][hapmap]
rs2392601	0.86[ASN][1000 genomes]
rs2392602	0.86[ASN][1000 genomes]
rs2392603	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392604	0.82[CEU][hapmap];0.98[ASN][1000 genomes]
rs2392605	0.94[ASN][1000 genomes]
rs2392606	0.94[ASN][1000 genomes]
rs2392607	0.96[ASN][1000 genomes]
rs28369620	0.98[ASN][1000 genomes]
rs28460817	0.96[ASN][1000 genomes]
rs28552512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2893568	0.80[ASN][1000 genomes]
rs3213659	0.82[CHB][hapmap]
rs3735346	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779122	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs3779124	0.81[ASN][1000 genomes]
rs3779125	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs3779127	0.82[CHB][hapmap]
rs3801113	1.00[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]
rs3801114	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801124	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801126	0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs3801127	0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs3801128	0.90[ASN][1000 genomes]
rs3801132	0.86[ASN][1000 genomes]
rs3801134	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs4623319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720306	0.83[ASN][1000 genomes]
rs4723791	0.84[ASN][1000 genomes]
rs4723792	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs4723795	0.86[ASN][1000 genomes]
rs4723796	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs4723800	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs56980069	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59626436	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59995998	1.00[ASN][1000 genomes]
rs62443565	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443566	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443575	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62444126	0.86[ASN][1000 genomes]
rs62444137	0.90[ASN][1000 genomes]
rs62444140	0.90[ASN][1000 genomes]
rs6415270	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs6462868	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs6462869	0.86[ASN][1000 genomes]
rs6462870	0.86[ASN][1000 genomes]
rs6943746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945239	0.98[ASN][1000 genomes]
rs6946636	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs6948026	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6955677	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6959858	0.90[ASN][1000 genomes]
rs6960585	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963364	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs6966738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968196	0.86[ASN][1000 genomes]
rs6969435	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs6973415	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6974795	0.98[ASN][1000 genomes]
rs73123612	0.90[ASN][1000 genomes]
rs73127433	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73131153	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7776996	0.98[ASN][1000 genomes]
rs7782927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788383	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793692	0.85[CEU][hapmap];0.96[ASN][1000 genomes]
rs7798033	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7803132	0.82[CHB][hapmap]
rs8180877	0.98[ASN][1000 genomes]
rs917320	1.00[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]
rs917321	1.00[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]
rs917322	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs929422	0.86[ASN][1000 genomes]
rs9639805	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs9655397	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs982392	0.82[CHB][hapmap];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830967	chr7:38913837-39069253	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3801111	CCDC32	trans	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr7:38889400-38948200	Weak transcription	Gastric	stomach
3	chr7:38906000-38947800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:38908800-38947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:38908800-38948000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:38909000-38947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:38911800-38948200	Weak transcription	Aorta	Aorta
8	chr7:38916800-38948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:38918800-38948000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:38921800-38947800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:38925200-38947800	Weak transcription	HUVEC	blood vessel
12	chr7:38926400-38948000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:38929200-38947800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:38930200-38947800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:38932200-38948000	Weak transcription	Psoas Muscle	Psoas
16	chr7:38932800-38948000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr7:38933000-38947800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:38933000-38948200	Weak transcription	Spleen	Spleen
19	chr7:38934000-38947800	Weak transcription	Brain Angular Gyrus	brain
20	chr7:38935800-38947800	Weak transcription	Fetal Stomach	stomach
21	chr7:38935800-38948000	Weak transcription	Placenta	Placenta
22	chr7:38935800-38948000	Weak transcription	Ovary	ovary
23	chr7:38936000-38947800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:38936000-38947800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:38936000-38947800	Weak transcription	Osteobl	bone
26	chr7:38936200-38948000	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:38936200-38948000	Weak transcription	Thymus	Thymus
28	chr7:38936400-38947800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:38936400-38947800	Weak transcription	Primary T cells from cord blood	blood
30	chr7:38936400-38947800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:38936400-38947800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr7:38936400-38948000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:38936400-38948000	Weak transcription	Fetal Intestine Large	intestine
34	chr7:38936400-38948000	Weak transcription	Fetal Thymus	thymus
35	chr7:38936600-38947800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr7:38936600-38947800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:38936800-38948000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:38938000-38947800	Weak transcription	Fetal Intestine Small	intestine
39	chr7:38942000-38948000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:38942000-38948000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:38942200-38948000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:38943000-38947800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:38943000-38947800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:38943000-38948000	Weak transcription	Left Ventricle	heart
45	chr7:38943000-38948000	Weak transcription	Lung	lung
46	chr7:38943000-38948000	Weak transcription	Pancreas	Pancrea
47	chr7:38943000-38948200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:38943200-38947800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:38943200-38948000	Weak transcription	HSMMtube	muscle
50	chr7:38943200-38948200	Weak transcription	Esophagus	oesophagus

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