Variant report

Variant	rs12593858
Chromosome Location	chr15:52607562-52607563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52584675..52589116-chr15:52605862..52610678,6	MCF-7	breast:
2	chr15:52606783..52608986-chr15:52658810..52661433,2	MCF-7	breast:
3	chr15:52606639..52609024-chr15:52615488..52617406,2	K562	blood:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10444827	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10851513	0.82[EUR][1000 genomes]
rs11633035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11637651	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638118	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638675	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs1534201	0.83[ASN][1000 genomes]
rs1626180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1632403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1669859	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1669865	0.86[AFR][1000 genomes]
rs1669871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669875	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1669876	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1693500	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1724584	0.86[AFR][1000 genomes]
rs1724586	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1724613	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1724617	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1724640	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1917972	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1967624	0.85[ASN][1000 genomes]
rs2444012	0.85[ASN][1000 genomes]
rs2444014	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2444017	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2444018	0.81[ASN][1000 genomes]
rs2462855	0.86[AFR][1000 genomes]
rs2693459	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2693467	1.00[CHB][hapmap]
rs59277991	0.86[AFR][1000 genomes]
rs62015995	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62015997	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016004	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62016006	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031817	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8035295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52593600-52608600	Weak transcription	Fetal Brain Male	brain
2	chr15:52595400-52610800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:52595400-52614200	Weak transcription	Fetal Lung	lung
4	chr15:52595600-52609800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:52595800-52628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:52596000-52608400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:52596000-52608800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:52596000-52611000	Weak transcription	Fetal Stomach	stomach
9	chr15:52596200-52623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:52596400-52608600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr15:52597600-52608600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:52597800-52629600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:52598400-52608400	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:52599200-52611000	Weak transcription	NHLF	lung
16	chr15:52599400-52611000	Weak transcription	Fetal Thymus	thymus
17	chr15:52599400-52611000	Weak transcription	Thymus	Thymus
18	chr15:52599800-52611000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:52599800-52611000	Weak transcription	A549	lung
20	chr15:52600400-52611200	Weak transcription	Colonic Mucosa	Colon
21	chr15:52600600-52611000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:52600600-52624200	Weak transcription	Liver	Liver
23	chr15:52600800-52622800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:52601000-52608600	Weak transcription	Brain Anterior Caudate	brain
26	chr15:52601000-52610000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:52601000-52611000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:52601000-52622600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:52601200-52611000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:52601200-52615200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:52601200-52622600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr15:52601400-52609800	Weak transcription	Gastric	stomach
34	chr15:52601400-52611000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:52601400-52611000	Weak transcription	Right Atrium	heart
36	chr15:52601400-52612200	Weak transcription	Right Ventricle	heart
37	chr15:52601600-52622400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:52601600-52622800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:52601800-52608400	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:52601800-52611000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:52601800-52611000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr15:52601800-52616600	Strong transcription	Primary B cells from cord blood	blood
43	chr15:52601800-52621400	Weak transcription	Psoas Muscle	Psoas
44	chr15:52602000-52608400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:52602000-52609400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr15:52602000-52609800	Weak transcription	Pancreas	Pancrea
47	chr15:52602000-52611000	Weak transcription	Esophagus	oesophagus
48	chr15:52602000-52622800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:52602200-52611000	Weak transcription	Fetal Heart	heart
50	chr15:52602200-52622600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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