Variant report

Variant	rs12623462
Chromosome Location	chr2:39977265-39977266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39975048..39977790-chr2:39997360..39998912,2	K562	blood:
2	chr2:39971834..39974291-chr2:39976414..39978177,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10164984	0.83[EUR][1000 genomes]
rs10169390	0.83[EUR][1000 genomes]
rs10174709	0.86[ASN][1000 genomes]
rs10206408	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1035138	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1035139	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124691	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11124692	0.87[EUR][1000 genomes]
rs12470473	0.84[ASN][1000 genomes]
rs12617624	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12620957	0.83[ASN][1000 genomes]
rs12623545	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12624217	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12712653	0.88[ASN][1000 genomes]
rs12712656	0.83[EUR][1000 genomes]
rs13026313	0.82[ASN][1000 genomes]
rs13400213	0.83[EUR][1000 genomes]
rs13401182	0.87[AMR][1000 genomes]
rs13425906	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13428837	0.83[EUR][1000 genomes]
rs1548877	0.88[ASN][1000 genomes]
rs17478972	0.83[EUR][1000 genomes]
rs1861243	0.81[EUR][1000 genomes]
rs1986876	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041735	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2058620	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2110656	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2192685	0.87[EUR][1000 genomes]
rs2373688	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2373689	0.88[ASN][1000 genomes]
rs2540226	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2540227	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2716704	0.83[ASN][1000 genomes]
rs2716727	0.82[ASN][1000 genomes]
rs2716729	0.81[ASN][1000 genomes]
rs2716730	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35761077	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732121	0.90[ASN][1000 genomes]
rs3732122	0.87[ASN][1000 genomes]
rs3902124	0.81[AMR][1000 genomes]
rs4365444	0.81[AMR][1000 genomes]
rs4644998	0.82[AMR][1000 genomes]
rs4670955	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670956	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670957	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4670958	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670959	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59756273	0.88[ASN][1000 genomes]
rs6544242	0.90[ASN][1000 genomes]
rs6719179	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6722610	0.83[EUR][1000 genomes]
rs6731026	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6731450	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6747842	0.92[ASN][1000 genomes]
rs6750252	0.91[ASN][1000 genomes]
rs6758453	0.93[ASN][1000 genomes]
rs727376	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7560642	0.88[ASN][1000 genomes]
rs7565954	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7581406	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7591296	0.83[ASN][1000 genomes]
rs7591347	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs917960	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs917962	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs917963	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9309042	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs962262	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997976	0.90[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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:39960400-39983000	Weak transcription	Stomach Mucosa	stomach
3	chr2:39961400-39984200	Weak transcription	Colonic Mucosa	Colon
4	chr2:39962200-39986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:39962200-39993200	Strong transcription	Liver	Liver
6	chr2:39962800-39980200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:39963200-39982000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:39964200-39977400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:39964200-39984200	Weak transcription	Psoas Muscle	Psoas
10	chr2:39964800-39983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:39965200-39980000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:39965200-39983000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:39965400-39984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:39966800-39980000	Weak transcription	Esophagus	oesophagus
17	chr2:39966800-39980200	Weak transcription	Lung	lung
18	chr2:39966800-39983200	Weak transcription	Spleen	Spleen
19	chr2:39967000-39981000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:39967000-39983000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:39967000-39983200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:39967000-39983400	Weak transcription	Aorta	Aorta
23	chr2:39967200-39983000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:39967600-39991200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:39970200-39978200	Weak transcription	GM12878-XiMat	blood
27	chr2:39970800-39983000	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:39971000-39980000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:39971000-39980000	Weak transcription	Left Ventricle	heart
30	chr2:39971000-39983000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:39971000-39983000	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
33	chr2:39971200-39978600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr2:39971400-39982400	Strong transcription	HSMM	muscle
35	chr2:39971600-39981000	Weak transcription	HUVEC	blood vessel
36	chr2:39971600-39998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:39971800-39980400	Weak transcription	NHLF	lung
38	chr2:39972200-39982400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:39972400-39998600	Strong transcription	HMEC	breast
40	chr2:39972400-39998800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:39972800-39978000	Weak transcription	Hela-S3	cervix
42	chr2:39973000-39998800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:39973600-39983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:39973600-39983600	Weak transcription	Pancreas	Pancrea
45	chr2:39974000-39979800	Weak transcription	NHEK	skin
46	chr2:39974200-39998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:39974600-39994000	Strong transcription	Fetal Thymus	thymus
48	chr2:39975000-39978600	Strong transcription	Primary T cells from cord blood	blood
49	chr2:39975000-39981400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:39975000-39998400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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