Variant report

Variant	rs2499855
Chromosome Location	chr1:161929761-161929762
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	chr1:161922486..161924980-chr1:161928759..161931643,3	K562	blood:
2	chr1:161925023..161927018-chr1:161928283..161930641,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NOS1AP-2	chr1:161929297-161929914	NONHSAT007206

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10733044	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737502	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10753645	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753666	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800068	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394070	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553444	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134690	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2134696	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2298019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341468	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2341479	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499856	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880055	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34312480	1.00[ASN][1000 genomes]
rs34461550	0.90[ASN][1000 genomes]
rs35621393	0.94[ASN][1000 genomes]
rs36080602	1.00[ASN][1000 genomes]
rs3767633	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300199	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579731	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4656335	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656339	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6427633	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427639	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667896	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685369	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6698065	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs71639910	0.98[ASN][1000 genomes]
rs7517386	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532448	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924777	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1007108	chr1:161925814-162002917	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161861600-161936000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:161897800-161940000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:161901400-161935400	Weak transcription	Fetal Lung	lung
4	chr1:161902800-161943400	Weak transcription	Esophagus	oesophagus
5	chr1:161903600-161930400	Weak transcription	Fetal Brain Female	brain
6	chr1:161904800-161956600	Weak transcription	Fetal Brain Male	brain
7	chr1:161906800-161932200	Weak transcription	Stomach Mucosa	stomach
8	chr1:161911000-161937200	Weak transcription	Gastric	stomach
9	chr1:161911600-161939400	Weak transcription	HepG2	liver
10	chr1:161912600-161941600	Weak transcription	Fetal Kidney	kidney
11	chr1:161913600-161931600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:161914000-161932000	Weak transcription	Aorta	Aorta
13	chr1:161915000-161930800	Weak transcription	HUVEC	blood vessel
14	chr1:161916200-161930400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:161916200-161935600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:161916800-161931200	Weak transcription	HSMMtube	muscle
17	chr1:161919600-161930800	Weak transcription	Psoas Muscle	Psoas
18	chr1:161924000-161931000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:161924200-161931600	Weak transcription	Brain Anterior Caudate	brain
20	chr1:161924200-161932200	Weak transcription	Brain Angular Gyrus	brain
21	chr1:161924400-161930800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:161924400-161931800	Weak transcription	A549	lung
23	chr1:161924600-161931600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:161924600-161931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:161924600-161931600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:161924600-161931600	Weak transcription	Small Intestine	intestine
27	chr1:161924600-161932000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:161925000-161931400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:161925000-161937600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:161925400-161931600	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:161925400-161932200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:161925600-161930200	Weak transcription	Lung	lung
33	chr1:161925600-161931600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:161925800-161931000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:161926000-161930600	Weak transcription	Fetal Stomach	stomach
36	chr1:161926200-161939400	Weak transcription	Fetal Heart	heart
37	chr1:161926200-161942200	Weak transcription	Right Ventricle	heart
38	chr1:161926400-161932000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:161926800-161932000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:161926800-161935200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:161927000-161933600	Strong transcription	Primary T cells from cord blood	blood
42	chr1:161927000-161944000	Weak transcription	Colonic Mucosa	Colon
43	chr1:161927200-161930800	Weak transcription	NHLF	lung
44	chr1:161927200-161931600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:161927400-161931000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:161927400-161933800	Strong transcription	Dnd41	blood
47	chr1:161927600-161930800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:161927600-161933800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr1:161927800-161930400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:161927800-161930600	Strong transcription	Primary T cells fromperipheralblood	blood

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