Variant report

Variant	rs2744972
Chromosome Location	chr6:34659054-34659055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34623901..34626181-chr6:34657612..34659436,2	MCF-7	breast:
2	chr6:34657528..34660560-chr6:34662754..34664755,3	MCF-7	breast:
3	chr6:34658536..34661755-chr6:34723904..34726636,3	MCF-7	breast:
4	chr6:34657888..34660088-chr6:34685697..34688432,2	MCF-7	breast:
5	chr6:34657778..34659720-chr6:34722705..34725050,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196821	Chromatin interaction
ENSG00000124562	Chromatin interaction
ENSG00000272288	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11752260	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756392	1.00[CEU][hapmap]
rs11759235	0.80[EUR][1000 genomes]
rs1555773	0.81[EUR][1000 genomes]
rs16894959	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs2092344	1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252551	0.81[YRI][hapmap]
rs2395607	1.00[CHD][hapmap]
rs2492859	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492863	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744937	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744938	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2744939	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744942	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744954	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744955	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744956	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744963	0.81[YRI][hapmap]
rs2744964	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744965	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744966	0.81[YRI][hapmap]
rs2744971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744977	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764203	0.83[EUR][1000 genomes]
rs2764204	0.83[EUR][1000 genomes]
rs2764205	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2814943	0.88[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814944	0.90[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2814948	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2814950	0.81[YRI][hapmap]
rs2814960	0.81[EUR][1000 genomes]
rs2814962	0.81[EUR][1000 genomes]
rs2814973	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814977	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814983	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814985	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814986	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814990	0.81[YRI][hapmap]
rs2814993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814996	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814998	0.81[YRI][hapmap]
rs2815003	0.81[YRI][hapmap]
rs2815005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28567450	0.84[EUR][1000 genomes]
rs3800457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][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]
rs3800461	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56693020	0.81[EUR][1000 genomes]
rs56930444	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59142559	0.81[EUR][1000 genomes]
rs61431557	0.84[EUR][1000 genomes]
rs6457790	0.84[EUR][1000 genomes]
rs6907508	1.00[ASN][1000 genomes]
rs6911549	0.81[EUR][1000 genomes]
rs6936177	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6938239	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755822	0.81[EUR][1000 genomes]
rs9462007	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9462012	0.82[EUR][1000 genomes]
rs9462014	1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs9462016	0.84[EUR][1000 genomes]
rs9462025	0.80[EUR][1000 genomes]
rs9469860	0.87[EUR][1000 genomes]
rs9469864	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9469890	0.80[EUR][1000 genomes]
rs9469895	0.80[EUR][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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv885794	chr6:34561585-34673149	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	33 gene(s)	inside rSNPs	diseases
12	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription 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	42 gene(s)	inside rSNPs	diseases
13	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv5255	chr6:34658569-34703563	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2744972	C6orf106	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34626000-34662000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:34626800-34662400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:34633000-34662800	Weak transcription	Aorta	Aorta
4	chr6:34634800-34663200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:34636400-34662200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:34639800-34662800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:34639800-34662800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:34641400-34662800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:34641800-34661200	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:34641800-34663200	Weak transcription	Gastric	stomach
11	chr6:34642200-34663000	Weak transcription	Thymus	Thymus
12	chr6:34643000-34661200	Weak transcription	Right Atrium	heart
13	chr6:34643000-34662800	Weak transcription	Stomach Mucosa	stomach
14	chr6:34647800-34660800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:34647800-34661000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:34647800-34662000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:34647800-34662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:34647800-34662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:34647800-34662600	Weak transcription	Ovary	ovary
20	chr6:34647800-34662800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:34647800-34662800	Weak transcription	HSMMtube	muscle
22	chr6:34648000-34662600	Weak transcription	Right Ventricle	heart
23	chr6:34648000-34662800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:34648400-34662000	Weak transcription	Brain Anterior Caudate	brain
25	chr6:34649200-34660200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr6:34649200-34660400	Weak transcription	Primary T cells from cord blood	blood
27	chr6:34649200-34662200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:34649200-34662600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:34649400-34660200	Weak transcription	NHEK	skin
30	chr6:34649400-34661600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:34649400-34661600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:34649400-34662000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:34649400-34662000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:34649400-34662000	Weak transcription	Osteobl	bone
35	chr6:34649400-34662400	Weak transcription	HSMM	muscle
36	chr6:34649600-34661000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:34649600-34661000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:34649600-34661000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:34649600-34662000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:34649800-34660400	Weak transcription	Fetal Intestine Small	intestine
41	chr6:34650600-34659200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:34652800-34660000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:34652800-34660000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr6:34652800-34661200	Weak transcription	Hela-S3	cervix
45	chr6:34652800-34662200	Weak transcription	A549	lung
46	chr6:34653000-34662000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:34654000-34660800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr6:34655400-34660000	Weak transcription	Dnd41	blood
49	chr6:34655400-34663000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:34656000-34659800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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