Variant report

Variant	rs62174407
Chromosome Location	chr2:152644213-152644214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152561295..152563975-chr2:152642386..152645984,4	K562	blood:
2	chr2:152561295..152563899-chr2:152643463..152645984,3	K562	blood:
3	chr2:152642402..152644764-chr2:152646088..152649513,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARL5A-1	chr2:152643937-152645761	NONHSAT074964
2	lnc-RIF1-2	chr2:152643813-152644509	NONHSAT074963

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction
ENSG00000183091	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10169098	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10172958	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10173570	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10174624	0.82[ASN][1000 genomes]
rs10179630	0.80[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10186879	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10190733	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10198509	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10204195	0.89[ASN][1000 genomes]
rs10210114	0.92[ASN][1000 genomes]
rs10497093	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12328396	0.85[ASN][1000 genomes]
rs12693126	0.91[EUR][1000 genomes]
rs12992632	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12994595	0.96[ASN][1000 genomes]
rs13384856	0.85[ASN][1000 genomes]
rs13386934	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13395294	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13396041	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13402710	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13404687	0.96[EUR][1000 genomes]
rs13408513	0.89[ASN][1000 genomes]
rs13414130	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13416266	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13421183	0.85[ASN][1000 genomes]
rs13428623	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830358	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830400	0.96[ASN][1000 genomes]
rs2030589	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2030590	0.80[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34629725	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36111287	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36141926	0.89[ASN][1000 genomes]
rs3768656	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4436952	0.92[ASN][1000 genomes]
rs4525690	0.89[ASN][1000 genomes]
rs62174408	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62174411	0.96[ASN][1000 genomes]
rs6433628	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729878	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6750638	0.92[ASN][1000 genomes]
rs6754783	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7560854	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7565109	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7591340	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152616800-152644400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:152616800-152662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:152617000-152669400	Weak transcription	Gastric	stomach
4	chr2:152619000-152677400	Weak transcription	Brain Substantia Nigra	brain
5	chr2:152622200-152661800	Weak transcription	Fetal Kidney	kidney
6	chr2:152623000-152680000	Weak transcription	Spleen	Spleen
7	chr2:152623400-152658800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:152623400-152659000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:152623600-152659000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:152624000-152662600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:152624400-152656800	Weak transcription	HepG2	liver
12	chr2:152625400-152660000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:152626800-152647000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:152628000-152654800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:152629000-152661800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:152631400-152652000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:152631400-152667200	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:152631600-152661800	Weak transcription	HMEC	breast
19	chr2:152631800-152648600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:152632000-152659000	Weak transcription	NHLF	lung
21	chr2:152632200-152656400	Weak transcription	NH-A	brain
22	chr2:152632200-152679200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:152632400-152649000	Weak transcription	Osteobl	bone
24	chr2:152632600-152652000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:152633000-152652200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:152633000-152662200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:152633400-152650400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:152634000-152648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:152634000-152665400	Weak transcription	Fetal Stomach	stomach
30	chr2:152634000-152683400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:152634200-152657000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:152634200-152661000	Weak transcription	A549	lung
33	chr2:152634600-152661800	Weak transcription	NHEK	skin
34	chr2:152634800-152658200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:152634800-152672200	Weak transcription	Right Ventricle	heart
36	chr2:152635600-152645000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:152635600-152659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr2:152636000-152662400	Weak transcription	Fetal Brain Female	brain
39	chr2:152636400-152649200	Weak transcription	GM12878-XiMat	blood
40	chr2:152636400-152659000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:152636400-152661800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:152636600-152661600	Weak transcription	Colonic Mucosa	Colon
43	chr2:152636800-152649000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:152637000-152657400	Weak transcription	Dnd41	blood
45	chr2:152637000-152657800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:152637000-152659000	Weak transcription	Fetal Brain Male	brain
47	chr2:152638000-152645800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:152638200-152653200	Weak transcription	Fetal Heart	heart
49	chr2:152638600-152644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:152638600-152644800	Weak transcription	Esophagus	oesophagus

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