Variant report

Variant	rs1743940
Chromosome Location	chr6:134560021-134560022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13203172	0.81[JPT][hapmap]
rs1621042	0.81[JPT][hapmap]
rs1631657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1631879	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053580	0.94[JPT][hapmap]
rs17063535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17063545	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17063554	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17063563	0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1743937	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1743938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1743939	1.00[ASW][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs1743941	0.84[AFR][1000 genomes]
rs1743942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1743945	0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs1743946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1763502	0.81[JPT][hapmap]
rs1763509	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1763510	0.83[JPT][hapmap]
rs4896028	0.81[JPT][hapmap]
rs4896029	0.84[ASN][1000 genomes]
rs57109798	0.95[ASN][1000 genomes]
rs62425170	1.00[ASN][1000 genomes]
rs62425189	1.00[ASN][1000 genomes]
rs62425190	1.00[ASN][1000 genomes]
rs744196	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs9385680	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9493857	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492292	chr6:134464255-135028540	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1026369	chr6:134468470-135122264	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv538444	chr6:134468470-135122264	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	nsv1018677	chr6:134512542-134638259	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv538445	chr6:134512542-134638259	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1023931	chr6:134512542-134668702	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv538446	chr6:134512542-134668702	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134551000-134564000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:134551400-134560200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:134551600-134561600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:134556400-134560200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:134557200-134560200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:134557200-134560200	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:134557200-134561400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:134557400-134560200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:134557400-134560200	Weak transcription	Right Atrium	heart
10	chr6:134557400-134561800	Enhancers	Brain Hippocampus Middle	brain
11	chr6:134557600-134560200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:134557600-134560200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:134557600-134560200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:134557600-134561600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:134557800-134560400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:134557800-134560400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:134557800-134561000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:134557800-134561600	Weak transcription	HMEC	breast
19	chr6:134557800-134562000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:134557800-134571000	Weak transcription	NH-A	brain
21	chr6:134558000-134560200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:134558000-134560200	Weak transcription	K562	blood
23	chr6:134558000-134561000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:134558000-134561400	Weak transcription	NHEK	skin
25	chr6:134558000-134561600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:134558000-134561600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:134558200-134560200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:134558200-134561600	Weak transcription	GM12878-XiMat	blood
29	chr6:134558400-134560200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr6:134558600-134560200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:134558600-134560200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:134558800-134560200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr6:134558800-134560200	Weak transcription	Pancreas	Pancrea
34	chr6:134559000-134561400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr6:134559200-134560400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr6:134559200-134560800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:134559200-134561000	Enhancers	Brain Germinal Matrix	brain
38	chr6:134559200-134561200	Enhancers	Brain Angular Gyrus	brain
39	chr6:134559200-134561200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr6:134559200-134561200	Enhancers	Brain Substantia Nigra	brain
41	chr6:134559200-134561200	Enhancers	HepG2	liver
42	chr6:134559200-134562400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:134559200-134563200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:134559400-134560400	Enhancers	NHDF-Ad	bronchial
45	chr6:134559400-134561000	Enhancers	Brain Cingulate Gyrus	brain
46	chr6:134559400-134562800	Enhancers	Primary B cells from peripheral blood	blood
47	chr6:134559600-134560600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:134559600-134562000	Enhancers	Adipose Nuclei	Adipose
49	chr6:134560000-134560200	Enhancers	Brain Anterior Caudate	brain
50	chr6:134560000-134560600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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