Variant report

Variant	rs1890999
Chromosome Location	chr1:225640076-225640077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225637801..225642696-chr1:225647950..225650939,4	K562	blood:
2	chr1:225633065..225638606-chr1:225639136..225643843,7	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10915831	0.84[EUR][1000 genomes]
rs12071529	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1222434	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1222439	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1336480	0.85[EUR][1000 genomes]
rs1360958	0.85[EUR][1000 genomes]
rs1764345	0.88[EUR][1000 genomes]
rs1764347	0.88[EUR][1000 genomes]
rs1771318	0.88[EUR][1000 genomes]
rs2185528	0.85[EUR][1000 genomes]
rs4653638	0.83[EUR][1000 genomes]
rs4653640	0.84[EUR][1000 genomes]
rs499385	0.85[EUR][1000 genomes]
rs6426075	0.86[EUR][1000 genomes]
rs72750896	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7545317	0.84[EUR][1000 genomes]
rs954534	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225633000-225640200	Enhancers	Fetal Thymus	thymus
2	chr1:225633600-225642000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:225634200-225642000	Weak transcription	K562	blood
4	chr1:225634600-225648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:225635000-225647800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:225635200-225641200	Weak transcription	Liver	Liver
7	chr1:225635400-225641800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:225635600-225641600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:225635600-225642000	Weak transcription	Pancreas	Pancrea
10	chr1:225636200-225650000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:225636400-225641600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:225636400-225641600	Weak transcription	NHLF	lung
13	chr1:225636400-225642000	Weak transcription	Right Atrium	heart
14	chr1:225636600-225640800	Enhancers	HepG2	liver
15	chr1:225636600-225641400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:225636600-225641600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:225636600-225641800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:225636600-225642000	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:225637200-225641600	Weak transcription	Osteobl	bone
20	chr1:225637400-225641400	Enhancers	Colon Smooth Muscle	Colon
21	chr1:225637600-225641800	Weak transcription	Small Intestine	intestine
22	chr1:225637800-225640200	Enhancers	Stomach Smooth Muscle	stomach
23	chr1:225637800-225641400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:225637800-225641400	Weak transcription	Stomach Mucosa	stomach
25	chr1:225637800-225642000	Weak transcription	Gastric	stomach
26	chr1:225637800-225642000	Weak transcription	Lung	lung
27	chr1:225637800-225647600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:225637800-225648400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:225638400-225640400	Enhancers	Fetal Stomach	stomach
30	chr1:225638800-225640200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:225638800-225641400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:225638800-225641400	Weak transcription	A549	lung
33	chr1:225638800-225642000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:225638800-225642000	Weak transcription	HUVEC	blood vessel
35	chr1:225638800-225642200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:225639000-225640200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:225639000-225641200	Weak transcription	Thymus	Thymus
38	chr1:225639000-225642200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:225639200-225641400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:225639200-225641400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:225639200-225641600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:225639200-225641800	Weak transcription	HSMMtube	muscle
43	chr1:225639400-225640200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:225639400-225641400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:225639400-225641400	Weak transcription	Hela-S3	cervix
46	chr1:225639400-225641600	Weak transcription	NHEK	skin
47	chr1:225639400-225647000	Weak transcription	Esophagus	oesophagus
48	chr1:225639400-225648000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:225639600-225641800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:225639600-225642000	Weak transcription	NH-A	brain

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