Variant report

Variant	rs3949519
Chromosome Location	chr6:101243450-101243451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101235770..101239248-chr6:101239414..101244156,4	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13437380	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055162	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2132170	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4839791	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58406648	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72610820	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72610821	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72610822	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741500	0.87[EUR][1000 genomes]
rs7760406	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846802	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9322111	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9322116	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322175	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9322222	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9377084	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9377140	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9377231	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9386226	1.00[EUR][1000 genomes]
rs9386229	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9386254	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390513	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9390581	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9390671	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9399637	1.00[EUR][1000 genomes]
rs9399638	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9399654	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399657	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399668	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9404029	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9404041	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9404055	0.88[CHB][hapmap]
rs9404058	0.85[CHB][hapmap]
rs9485236	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9485306	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9498017	1.00[EUR][1000 genomes]
rs9498063	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9498203	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9498392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9498397	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv886456	chr6:101049108-101277926	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv604275	chr6:101158950-101277926	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1016353	chr6:101172705-101304041	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101184400-101304600	Weak transcription	Hela-S3	cervix
2	chr6:101191400-101277000	Weak transcription	Esophagus	oesophagus
3	chr6:101212000-101246400	Weak transcription	Psoas Muscle	Psoas
4	chr6:101212000-101276200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:101212000-101281400	Weak transcription	Aorta	Aorta
6	chr6:101213400-101244000	Weak transcription	HSMMtube	muscle
7	chr6:101213600-101256000	Weak transcription	Ovary	ovary
8	chr6:101213600-101281600	Weak transcription	Gastric	stomach
9	chr6:101213800-101250800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:101213800-101254200	Weak transcription	Fetal Thymus	thymus
11	chr6:101214800-101281600	Weak transcription	Left Ventricle	heart
12	chr6:101215200-101244000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:101215200-101244000	Weak transcription	Liver	Liver
14	chr6:101215200-101244000	Weak transcription	Placenta	Placenta
15	chr6:101215200-101247000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:101215200-101252600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:101215200-101256200	Weak transcription	Osteobl	bone
18	chr6:101215200-101263000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:101215200-101311400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:101215400-101243600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:101215400-101243600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:101215400-101244000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:101215400-101244000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:101215400-101258600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:101223000-101244200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:101223000-101256800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:101223400-101243600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:101226000-101243600	Weak transcription	HSMM	muscle
29	chr6:101226000-101281400	Weak transcription	HUVEC	blood vessel
30	chr6:101232000-101255200	Weak transcription	NHLF	lung
31	chr6:101233400-101244000	Weak transcription	HMEC	breast
32	chr6:101233600-101306600	Weak transcription	K562	blood
33	chr6:101233800-101265200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:101234200-101244000	Weak transcription	Adipose Nuclei	Adipose
35	chr6:101234400-101254400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:101234600-101260000	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:101235200-101246000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:101235800-101246000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr6:101236200-101245800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:101236800-101257800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:101237000-101257400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:101237600-101244200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:101237800-101244000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:101238000-101244200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:101238000-101251000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:101238000-101296200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:101238800-101257200	Weak transcription	HepG2	liver
48	chr6:101239400-101245000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:101239400-101254600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:101239800-101257800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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