Variant report

Variant	rs1000598
Chromosome Location	chr15:62141611-62141612
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62139945..62141808-chr15:62207864..62210759,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2CD4A-2	chr15:62141596-62141671	ENSG00000259564.1
2	lnc-C2CD4A-2	chr15:62141163-62142028	NONHSAT044261

Variant related genes	Relation type
ENSG00000129003	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10851703	0.86[EUR][1000 genomes]
rs10851704	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs10851705	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11071634	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11071635	0.86[CEU][hapmap]
rs11071641	0.82[CEU][hapmap]
rs11071647	0.89[CEU][hapmap]
rs11629528	0.82[CEU][hapmap]
rs11631013	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs11631970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11632774	0.82[EUR][1000 genomes]
rs11634516	0.85[CEU][hapmap]
rs11636504	0.84[EUR][1000 genomes]
rs11638344	0.84[EUR][1000 genomes]
rs12438431	0.86[CEU][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs12439330	0.84[EUR][1000 genomes]
rs12708468	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12708469	0.84[EUR][1000 genomes]
rs12708470	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898209	0.85[CEU][hapmap]
rs12901171	0.85[EUR][1000 genomes]
rs12901481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12902092	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs12902409	0.84[EUR][1000 genomes]
rs12908081	0.85[CEU][hapmap]
rs12909692	0.81[EUR][1000 genomes]
rs12915825	0.80[AMR][1000 genomes]
rs12916268	0.80[AMR][1000 genomes]
rs13379947	0.89[CEU][hapmap]
rs1346036	0.86[EUR][1000 genomes]
rs1364810	0.82[CEU][hapmap]
rs1370177	0.85[CEU][hapmap]
rs1425270	0.82[JPT][hapmap]
rs17205225	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17271151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17271235	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1981916	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs1981917	0.80[AMR][1000 genomes]
rs1991205	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs2042610	0.83[CEU][hapmap]
rs2059471	0.82[EUR][1000 genomes]
rs2098850	0.84[EUR][1000 genomes]
rs2113932	0.86[CEU][hapmap]
rs2113933	0.86[CEU][hapmap]
rs2162064	0.82[CEU][hapmap]
rs2241491	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2414755	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs28413840	0.85[EUR][1000 genomes]
rs3743294	0.83[CEU][hapmap]
rs3743297	0.85[CEU][hapmap]
rs3809517	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3886246	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs4283171	0.80[AMR][1000 genomes]
rs4541010	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs4587915	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs4774425	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs4775442	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs4775445	0.84[YRI][hapmap]
rs4775447	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs4775451	0.85[EUR][1000 genomes]
rs4775453	0.85[CEU][hapmap]
rs6494299	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs7163441	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs7164933	0.92[CEU][hapmap]
rs7166891	0.83[JPT][hapmap]
rs7168164	0.85[CEU][hapmap]
rs7402374	0.84[EUR][1000 genomes]
rs8025282	0.86[EUR][1000 genomes]
rs8033816	0.81[YRI][hapmap]
rs8034185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788670	0.81[CEU][hapmap]
rs9920945	0.86[EUR][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	nsv904284	chr15:62123600-62243197	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62132400-62159000	Weak transcription	HSMM	muscle
2	chr15:62132400-62171200	Weak transcription	HMEC	breast
3	chr15:62132800-62146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:62134000-62144200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr15:62135000-62161600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:62136800-62150000	Weak transcription	HSMMtube	muscle
7	chr15:62137200-62144800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:62137400-62143400	Weak transcription	Adipose Nuclei	Adipose
9	chr15:62137400-62145400	Weak transcription	Liver	Liver
10	chr15:62138400-62143200	Weak transcription	Primary T cells from cord blood	blood
11	chr15:62138800-62142600	Weak transcription	Left Ventricle	heart
12	chr15:62138800-62184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:62139200-62143400	Weak transcription	Primary B cells from cord blood	blood
14	chr15:62139200-62144000	Weak transcription	Lung	lung
15	chr15:62139200-62146000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:62139200-62146600	Weak transcription	Pancreas	Pancrea
17	chr15:62139200-62182200	Weak transcription	Brain Substantia Nigra	brain
18	chr15:62139400-62143200	Weak transcription	Fetal Intestine Small	intestine
19	chr15:62139400-62154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:62139600-62142000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:62139600-62143600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:62139600-62145400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:62139800-62185200	Weak transcription	NHLF	lung
24	chr15:62140000-62143200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr15:62140000-62143200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:62140000-62143200	Weak transcription	NHDF-Ad	bronchial
27	chr15:62140000-62144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:62140000-62184800	Weak transcription	Right Ventricle	heart
29	chr15:62140200-62180000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:62140400-62143400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:62140400-62145800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:62140600-62142400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:62140600-62143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:62140800-62143200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr15:62140800-62143400	Weak transcription	Fetal Intestine Large	intestine
36	chr15:62140800-62143800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:62140800-62146400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:62140800-62149000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:62141000-62143400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:62141000-62144000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:62141000-62149400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:62141200-62149600	Weak transcription	Psoas Muscle	Psoas
43	chr15:62141200-62165400	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:62141400-62143400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:62141400-62144000	Weak transcription	Dnd41	blood
46	chr15:62141400-62146600	Weak transcription	GM12878-XiMat	blood
47	chr15:62141400-62160600	Weak transcription	Placenta	Placenta
48	chr15:62141400-62161400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:62141600-62146200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:62141600-62146400	Weak transcription	Rectal Mucosa Donor 29	rectum

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