Variant report

Variant	rs7554788
Chromosome Location	chr1:197550676-197550677
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11799366	1.00[AMR][1000 genomes]
rs11800199	1.00[AMR][1000 genomes]
rs11801895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802844	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11802940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11803371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11803914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11805327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11805399	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11805755	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11805812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11805909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11806221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11806278	1.00[AMR][1000 genomes]
rs11806385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11806492	1.00[AFR][1000 genomes]
rs11806557	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11806645	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11806651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11806821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11806872	1.00[AFR][1000 genomes]
rs11807556	1.00[AMR][1000 genomes]
rs11807717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11808659	0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11809220	1.00[AMR][1000 genomes]
rs11809987	1.00[AMR][1000 genomes]
rs11810711	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11811376	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841475	1.00[AMR][1000 genomes]
rs16841531	1.00[AMR][1000 genomes]
rs16841850	1.00[AMR][1000 genomes]
rs16841865	1.00[AMR][1000 genomes]
rs16841889	1.00[AMR][1000 genomes]
rs34240488	1.00[AMR][1000 genomes]
rs35781299	1.00[AMR][1000 genomes]
rs3888103	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6428399	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6428400	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6657488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6666890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6667162	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6667565	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6697556	1.00[AMR][1000 genomes]
rs6698391	1.00[AFR][1000 genomes]
rs6703514	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7522037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7533154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7535981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7543290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9661515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9727335	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv548872	chr1:197529218-197644581	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3397065	chr1:197545083-197637033	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197506800-197564600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:197508400-197602400	Weak transcription	Left Ventricle	heart
3	chr1:197526800-197563000	Weak transcription	Osteobl	bone
4	chr1:197537000-197574600	Weak transcription	NHDF-Ad	bronchial
5	chr1:197537400-197602200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:197537800-197585600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:197538000-197554000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:197538600-197563600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:197539000-197554400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:197539000-197556600	Weak transcription	Fetal Kidney	kidney
11	chr1:197540000-197554600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:197541800-197551000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:197541800-197566000	Weak transcription	Ovary	ovary
14	chr1:197541800-197602400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:197541800-197602600	Weak transcription	Fetal Thymus	thymus
16	chr1:197542000-197552200	Weak transcription	Primary T cells from cord blood	blood
17	chr1:197542000-197554000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:197542000-197555800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:197542000-197557000	Weak transcription	Fetal Intestine Small	intestine
20	chr1:197542000-197559600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:197542000-197559800	Weak transcription	Liver	Liver
22	chr1:197542000-197568000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:197542000-197569200	Weak transcription	Pancreas	Pancrea
24	chr1:197542000-197571400	Weak transcription	Esophagus	oesophagus
25	chr1:197542000-197574400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:197542000-197609000	Weak transcription	Colonic Mucosa	Colon
27	chr1:197542000-197626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:197542600-197563200	Weak transcription	Fetal Heart	heart
29	chr1:197544000-197553600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:197544000-197562000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:197544400-197602400	Weak transcription	Primary B cells from cord blood	blood
32	chr1:197544600-197570000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:197545400-197552600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:197545600-197551800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:197545600-197553200	Strong transcription	Dnd41	blood
36	chr1:197545600-197567400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:197546000-197552000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:197546800-197551000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:197547000-197552000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:197547000-197587200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:197547400-197602400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:197547600-197566200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:197548600-197553200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:197548600-197569400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:197549600-197550800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:197550200-197551400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:197550200-197552000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr1:197550400-197552600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:197550400-197552600	Strong transcription	Fetal Lung	lung
50	chr1:197550400-197553000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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