Variant report

Variant	rs2744942
Chromosome Location	chr6:34643752-34643753
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	chr6:34638896..34641343-chr6:34641586..34643801,2	MCF-7	breast:
2	chr6:34638012..34641367-chr6:34642120..34645607,4	K562	blood:

Variant related genes	Relation type
ENSG00000196821	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11752260	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756392	1.00[CEU][hapmap]
rs16894959	1.00[CEU][hapmap]
rs2092344	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252551	0.81[YRI][hapmap]
rs2492859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492863	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744937	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744938	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2744939	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744947	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744954	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744955	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744956	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.94[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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744965	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744972	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]
rs2744977	0.90[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764205	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2814943	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814944	0.90[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814948	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814973	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814977	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814983	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814985	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814986	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814990	0.81[YRI][hapmap]
rs2814993	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814996	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815003	0.81[YRI][hapmap]
rs2815005	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28567450	0.80[EUR][1000 genomes]
rs3800457	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]
rs3800461	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56930444	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457790	0.80[EUR][1000 genomes]
rs6907508	1.00[ASN][1000 genomes]
rs6936177	1.00[CEU][hapmap]
rs6938239	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462007	1.00[CEU][hapmap]
rs9462016	0.80[EUR][1000 genomes]
rs9469860	0.83[EUR][1000 genomes]
rs9469864	1.00[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2744942	C6orf106	Cis_1M	lymphoblastoid	RTeQTL
rs2744942	C6orf107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34626000-34647600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:34626000-34662000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:34626800-34662400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:34632600-34647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:34632800-34655200	Weak transcription	Fetal Stomach	stomach
6	chr6:34633000-34662800	Weak transcription	Aorta	Aorta
7	chr6:34634800-34663200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:34635800-34647400	Weak transcription	Brain Angular Gyrus	brain
9	chr6:34636400-34662200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:34638600-34644200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:34639800-34644600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:34639800-34648600	Weak transcription	HSMM	muscle
13	chr6:34639800-34662800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:34639800-34662800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:34640000-34647400	Weak transcription	HSMMtube	muscle
16	chr6:34640000-34647600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:34640200-34647400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:34640200-34647400	Weak transcription	NH-A	brain
19	chr6:34640200-34648800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:34640200-34656600	Weak transcription	Spleen	Spleen
21	chr6:34640800-34655800	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:34641200-34644400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr6:34641400-34643800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr6:34641400-34644000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr6:34641400-34644200	Enhancers	Primary T cells from cord blood	blood
26	chr6:34641400-34646800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:34641400-34647400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:34641400-34647400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:34641400-34647600	Weak transcription	Brain Anterior Caudate	brain
30	chr6:34641400-34647600	Weak transcription	A549	lung
31	chr6:34641400-34662800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:34641600-34643800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr6:34641600-34644200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr6:34641600-34644200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr6:34641600-34644400	Enhancers	Primary B cells from peripheral blood	blood
36	chr6:34641600-34644400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr6:34641600-34644400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:34641600-34644400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:34641600-34644600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:34641600-34644800	Enhancers	Primary B cells from cord blood	blood
41	chr6:34641600-34647000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:34641600-34647400	Weak transcription	Ovary	ovary
43	chr6:34641600-34647400	Weak transcription	Psoas Muscle	Psoas
44	chr6:34641600-34647400	Weak transcription	Small Intestine	intestine
45	chr6:34641600-34654800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:34641600-34654800	Weak transcription	Dnd41	blood
47	chr6:34641600-34655400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:34641800-34644000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:34641800-34646800	Weak transcription	Fetal Heart	heart
50	chr6:34641800-34647000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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