Variant report

Variant	rs200199
Chromosome Location	chr6:5443815-5443816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12192898	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1364555	0.90[JPT][hapmap]
rs17133279	0.90[JPT][hapmap]
rs17140384	0.90[JPT][hapmap]
rs17140394	0.90[JPT][hapmap]
rs183221	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs183222	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs200194	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs200195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs200196	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs200197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs200202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2432780	0.90[JPT][hapmap]
rs2432785	0.90[JPT][hapmap]
rs2432786	0.90[JPT][hapmap]
rs2432788	0.88[JPT][hapmap]
rs2503818	0.90[JPT][hapmap]
rs2503823	0.90[JPT][hapmap]
rs2503835	0.90[JPT][hapmap]
rs2552289	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2791458	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003869	0.90[JPT][hapmap]
rs554425	0.90[ASN][1000 genomes]
rs656078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72817717	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760235	0.90[JPT][hapmap]
rs9502295	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1015643	chr6:5311590-5452427	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1030744	chr6:5328012-5458222	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1022505	chr6:5388025-5449240	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv600885	chr6:5424762-5455161	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv600886	chr6:5426265-5511614	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5403400-5445200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:5421600-5455000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:5421600-5455400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:5421600-5457400	Weak transcription	Fetal Intestine Small	intestine
5	chr6:5422800-5444000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:5433400-5453800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:5433600-5457400	Weak transcription	Left Ventricle	heart
8	chr6:5433600-5461400	Weak transcription	Fetal Stomach	stomach
9	chr6:5434200-5487000	Weak transcription	Aorta	Aorta
10	chr6:5436400-5446600	Weak transcription	HSMM	muscle
11	chr6:5436400-5447200	Weak transcription	HSMMtube	muscle
12	chr6:5437400-5471200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:5438200-5445800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:5438200-5471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:5439600-5459800	Weak transcription	Primary T cells from cord blood	blood
16	chr6:5440400-5454800	Weak transcription	Liver	Liver
17	chr6:5441000-5444800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:5442800-5444000	Enhancers	Fetal Lung	lung
19	chr6:5443000-5457200	Weak transcription	Brain Anterior Caudate	brain
20	chr6:5443200-5444400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr6:5443200-5445800	Weak transcription	Hela-S3	cervix
22	chr6:5443200-5446600	Weak transcription	Osteobl	bone
23	chr6:5443400-5444000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:5443400-5444000	Enhancers	Brain Hippocampus Middle	brain
25	chr6:5443600-5444000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:5443600-5444000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr6:5443600-5444000	Enhancers	Esophagus	oesophagus
28	chr6:5443600-5444000	Enhancers	Pancreas	Pancrea
29	chr6:5443600-5444000	Enhancers	Right Atrium	heart
30	chr6:5443600-5444000	Enhancers	Right Ventricle	heart
31	chr6:5443600-5444000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:5443600-5444400	Enhancers	Gastric	stomach
33	chr6:5443600-5444400	Enhancers	Psoas Muscle	Psoas
34	chr6:5443600-5444400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr6:5443600-5445000	Enhancers	Fetal Muscle Leg	muscle
36	chr6:5443600-5446800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:5443800-5444000	Enhancers	Fetal Thymus	thymus
38	chr6:5443800-5444000	ZNF genes & repeats	Lung	lung
39	chr6:5443800-5444200	Enhancers	Primary B cells from cord blood	blood
40	chr6:5443800-5444400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:5443800-5444400	Enhancers	Fetal Brain Male	brain
42	chr6:5443800-5444400	Enhancers	Fetal Muscle Trunk	muscle
43	chr6:5443800-5458200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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