Variant report

Variant	rs9496939
Chromosome Location	chr6:144673443-144673444
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11970041	0.91[AMR][1000 genomes]
rs12178630	1.00[AMR][1000 genomes]
rs17073670	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2223428	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2328570	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28737224	0.91[AMR][1000 genomes]
rs6570620	1.00[AMR][1000 genomes]
rs6570621	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6902637	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6932679	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7768531	0.85[AFR][1000 genomes]
rs9321971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484866	1.00[AMR][1000 genomes]
rs9484868	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484869	0.91[AMR][1000 genomes]
rs9484870	0.91[AMR][1000 genomes]
rs9496929	1.00[AMR][1000 genomes]
rs9496933	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496934	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496940	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496941	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496942	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496943	0.83[AFR][1000 genomes]
rs9496945	0.87[AFR][1000 genomes]
rs9496946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496947	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144653200-144684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:144663200-144685800	Weak transcription	Brain Substantia Nigra	brain
3	chr6:144663400-144675200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:144665400-144696400	Weak transcription	Fetal Intestine Small	intestine
5	chr6:144667600-144674800	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:144668800-144681600	Weak transcription	Small Intestine	intestine
7	chr6:144670400-144674000	Flanking Active TSS	Dnd41	blood
8	chr6:144670400-144674200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr6:144670400-144674200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr6:144670800-144673600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr6:144670800-144673800	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr6:144670800-144673800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr6:144670800-144673800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:144670800-144674200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr6:144670800-144691200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:144671000-144681600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:144671000-144683200	Weak transcription	Gastric	stomach
18	chr6:144671200-144673600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:144671200-144674800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:144671200-144675200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:144671200-144692000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:144671400-144675200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:144671400-144675400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:144671400-144681600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:144671400-144681600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:144671600-144673600	Weak transcription	Fetal Kidney	kidney
27	chr6:144671600-144675400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:144671800-144673800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:144671800-144673800	Enhancers	Fetal Thymus	thymus
30	chr6:144671800-144675200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:144671800-144681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:144671800-144683200	Weak transcription	HSMM	muscle
33	chr6:144671800-144685200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:144672000-144674200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:144672000-144676000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr6:144672000-144683200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:144672200-144676200	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:144672400-144673600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:144672400-144673800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr6:144672400-144673800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr6:144672400-144673800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:144672600-144673800	Enhancers	Fetal Muscle Leg	muscle
43	chr6:144672600-144673800	Enhancers	NHDF-Ad	bronchial
44	chr6:144672600-144673800	Enhancers	Osteobl	bone
45	chr6:144672600-144674200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:144672600-144674400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:144673000-144673600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:144673000-144673800	Enhancers	NH-A	brain
49	chr6:144673000-144675400	Enhancers	Primary hematopoietic stem cells	blood
50	chr6:144673000-144681400	Weak transcription	Esophagus	oesophagus

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