Variant report

Variant	rs2079998
Chromosome Location	chr2:37865070-37865071
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	chr2:37859378..37862018-chr2:37863759..37867582,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-QPCT-3	chr2:37832379-37870742	NONHSAT070127
2	lnc-QPCT-3	chr2:37864557-37865599	NONHSAT070132

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1013291	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1013292	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12622958	0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13387842	0.88[ASN][1000 genomes]
rs13392288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406302	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13417833	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13417957	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1468663	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468664	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17021174	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2041508	0.90[ASN][1000 genomes]
rs2072419	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2098198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109822	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159726	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373290	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373292	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3731852	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3731854	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4372883	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4594425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670210	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs4670748	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs6544095	0.87[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs6711909	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs6740127	0.84[ASN][1000 genomes]
rs6752119	0.91[CHB][hapmap]
rs6752220	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6752762	0.90[ASN][1000 genomes]
rs6759224	0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs7607934	0.86[JPT][hapmap];0.92[MEX][hapmap]
rs7735	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9742	0.88[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456374	chr2:37669487-37868214	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv470453	chr2:37669487-37868214	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv581473	chr2:37669487-37868214	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37873200	Weak transcription	Liver	Liver
2	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
3	chr2:37857000-37871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:37857200-37865200	Weak transcription	Left Ventricle	heart
5	chr2:37857200-37865800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:37857200-37868200	Weak transcription	Psoas Muscle	Psoas
7	chr2:37858000-37868600	Weak transcription	A549	lung
8	chr2:37858400-37867600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:37858800-37871400	Weak transcription	Aorta	Aorta
10	chr2:37859000-37868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:37859200-37868600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:37860000-37871200	Weak transcription	Gastric	stomach
13	chr2:37860200-37866800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:37860200-37868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:37860400-37865600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:37860400-37865600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:37860400-37867400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:37860800-37867000	Weak transcription	NHLF	lung
19	chr2:37860800-37873000	Weak transcription	Pancreas	Pancrea
20	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:37861000-37865600	Enhancers	Fetal Thymus	thymus
22	chr2:37861000-37868000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:37861800-37866200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:37862000-37865600	Enhancers	Thymus	Thymus
25	chr2:37862000-37866600	Enhancers	HSMM	muscle
26	chr2:37862000-37867000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:37862000-37869400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:37862200-37865600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:37862200-37866800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:37862200-37867000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:37862200-37867200	Enhancers	NHDF-Ad	bronchial
32	chr2:37862200-37870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:37862400-37869200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:37862400-37870200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:37862600-37865200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:37862600-37865600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:37862800-37869400	Weak transcription	HUVEC	blood vessel
38	chr2:37863200-37868200	Weak transcription	Right Atrium	heart
39	chr2:37863400-37868000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:37863400-37868200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:37863400-37875000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:37863600-37865200	Weak transcription	Esophagus	oesophagus
43	chr2:37863600-37865600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:37863600-37865600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:37863600-37866600	Enhancers	HSMMtube	muscle
46	chr2:37863600-37867000	Weak transcription	NH-A	brain
47	chr2:37863600-37868200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:37863600-37868200	Weak transcription	HMEC	breast
49	chr2:37863600-37868400	Weak transcription	NHEK	skin
50	chr2:37863600-37868800	Weak transcription	Fetal Brain Female	brain

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