Variant report

Variant	rs479661
Chromosome Location	chr2:169721377-169721378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2461385	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2685800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2685801	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475467	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs477309	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs494859	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs498041	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs499160	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs504393	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs509988	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511778	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs525428	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs533492	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534771	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs539400	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560494	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576338	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs577192	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs580507	0.98[EUR][1000 genomes]
rs581363	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][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	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv875381	chr2:169686559-169749841	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv516627	chr2:169714893-169721377	Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169689000-169721800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:169693400-169721400	Weak transcription	Spleen	Spleen
3	chr2:169693600-169721400	Weak transcription	Right Ventricle	heart
4	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:169702600-169721400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:169704200-169723400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:169704600-169721400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:169705000-169723600	Weak transcription	Fetal Brain Female	brain
10	chr2:169705200-169721400	Weak transcription	Fetal Kidney	kidney
11	chr2:169706600-169721600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:169706600-169727800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:169707400-169722000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:169708600-169723200	Weak transcription	NHLF	lung
15	chr2:169709200-169721400	Weak transcription	HUVEC	blood vessel
16	chr2:169709800-169733400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:169710200-169721400	Weak transcription	NHEK	skin
18	chr2:169711400-169721600	Weak transcription	NH-A	brain
19	chr2:169712600-169727800	Weak transcription	Primary T cells from cord blood	blood
20	chr2:169713200-169728800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:169713400-169722000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:169713400-169731200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:169713600-169722000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:169714000-169732800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:169714200-169722000	Strong transcription	Dnd41	blood
26	chr2:169714400-169721400	Strong transcription	Adipose Nuclei	Adipose
27	chr2:169714400-169722200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:169715200-169721600	Strong transcription	Fetal Intestine Large	intestine
29	chr2:169715400-169731600	Weak transcription	Small Intestine	intestine
30	chr2:169715400-169746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:169716000-169722000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:169716000-169745800	Weak transcription	HSMM	muscle
33	chr2:169717000-169722200	Strong transcription	Fetal Thymus	thymus
34	chr2:169717000-169727200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:169717000-169746400	Weak transcription	Primary B cells from cord blood	blood
36	chr2:169717600-169721600	Strong transcription	Pancreas	Pancrea
37	chr2:169717600-169722000	Strong transcription	Thymus	Thymus
38	chr2:169718000-169721400	Weak transcription	Brain Germinal Matrix	brain
39	chr2:169718400-169721800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:169718600-169721600	Strong transcription	Left Ventricle	heart
41	chr2:169718600-169722000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:169719000-169721400	Weak transcription	Fetal Heart	heart
43	chr2:169719000-169722000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:169719200-169723600	Weak transcription	Ovary	ovary
45	chr2:169719600-169721400	Weak transcription	Gastric	stomach
46	chr2:169719600-169722200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:169719800-169733600	Weak transcription	NHDF-Ad	bronchial
48	chr2:169720000-169724800	Weak transcription	Osteobl	bone
49	chr2:169720200-169722000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:169720200-169723000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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