Variant report

Variant	rs2552301
Chromosome Location	chr6:5327560-5327561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2552300	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753253	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753254	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763182	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs55716067	0.88[ASN][1000 genomes]
rs62386863	0.88[ASN][1000 genomes]
rs62386900	0.85[ASN][1000 genomes]
rs708036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72815645	0.83[ASN][1000 genomes]
rs7774214	0.82[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs797128	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs797131	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs809962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9378421	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9378422	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs9378946	0.81[ASN][1000 genomes]
rs9392079	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs9392676	0.85[ASN][1000 genomes]
rs9392678	0.80[ASN][1000 genomes]
rs9405818	0.81[JPT][hapmap]
rs9405819	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9405820	0.84[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9405821	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs9405824	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9405826	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9405828	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9405829	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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 miRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	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
16	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
17	nsv1028185	chr6:5247624-5340163	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	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
19	nsv1022738	chr6:5298362-5411645	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv600883	chr6:5302619-5400658	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv883417	chr6:5307432-5431340	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	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
23	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
24	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
25	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
26	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
27	nsv883419	chr6:5316399-5400658	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5288400-5331000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:5292800-5334400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:5303200-5368800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:5303600-5332400	Weak transcription	Gastric	stomach
5	chr6:5304000-5337600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:5309200-5333400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:5309200-5334000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:5316400-5333800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:5316800-5335200	Weak transcription	NHLF	lung
10	chr6:5318800-5331600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:5319200-5328200	Weak transcription	Thymus	Thymus
12	chr6:5319600-5334600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:5320600-5344400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:5321400-5327600	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:5321800-5335200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:5322200-5333800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:5322600-5333600	Weak transcription	A549	lung
18	chr6:5323000-5327600	Weak transcription	Liver	Liver
19	chr6:5323000-5331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:5323800-5327600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:5324600-5327800	Weak transcription	Dnd41	blood
22	chr6:5324800-5334000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:5325000-5327800	Strong transcription	Primary T cells from cord blood	blood
24	chr6:5325000-5331600	Weak transcription	Right Ventricle	heart
25	chr6:5325200-5335000	Weak transcription	Fetal Lung	lung
26	chr6:5325600-5328000	Weak transcription	Psoas Muscle	Psoas
27	chr6:5325600-5328600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:5325600-5329200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:5325800-5328800	Weak transcription	Ovary	ovary
30	chr6:5325800-5331600	Weak transcription	Adipose Nuclei	Adipose
31	chr6:5325800-5331600	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:5325800-5334000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:5325800-5334000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:5325800-5339600	Weak transcription	Fetal Intestine Large	intestine
35	chr6:5326000-5333600	Weak transcription	HepG2	liver
36	chr6:5326000-5335400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:5326000-5337800	Weak transcription	HSMM	muscle
38	chr6:5326400-5337800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:5326600-5328400	Weak transcription	Brain Substantia Nigra	brain
40	chr6:5326600-5349200	Weak transcription	Primary B cells from cord blood	blood
41	chr6:5326600-5385000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:5326800-5328400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr6:5326800-5328400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:5326800-5330000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:5326800-5334000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:5326800-5337800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:5327000-5328800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:5327000-5328800	Weak transcription	K562	blood
49	chr6:5327000-5329800	Weak transcription	Pancreas	Pancrea
50	chr6:5327000-5334400	Weak transcription	Fetal Stomach	stomach

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