Variant report

Variant	rs2404972
Chromosome Location	chr15:76602212-76602213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:76589441..76591088-chr15:76601198..76602843,2	K562	blood:
2	chr15:76582923..76594852-chr15:76601949..76606997,18	MCF-7	breast:
3	chr15:76517181..76519721-chr15:76602211..76604425,2	K562	blood:
4	chr15:76579019..76580557-chr15:76600815..76603366,2	K562	blood:
5	chr15:76601574..76614388-chr15:76623703..76634730,38	K562	blood:
6	chr15:76600511..76607655-chr15:76613791..76629933,32	MCF-7	breast:
7	chr15:76584135..76596152-chr15:76600630..76606670,15	MCF-7	breast:
8	chr15:76601310..76610583-chr15:76618699..76634643,40	K562	blood:

No data

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction
ENSG00000159556	Chromatin interaction
ENSG00000259514	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11856717	0.84[CEU][hapmap];0.86[AFR][1000 genomes]
rs12437866	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12441111	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16967947	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs35827241	1.00[AFR][1000 genomes]
rs4886489	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4886794	1.00[CEU][hapmap]
rs4886804	0.81[CEU][hapmap]
rs62027052	0.96[ASN][1000 genomes]
rs62027056	0.93[ASN][1000 genomes]
rs7171795	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520069	chr15:76602212-76609181	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2404972	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2404972	ISL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76558000-76603000	Weak transcription	Aorta	Aorta
2	chr15:76576200-76602800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:76584600-76602400	Weak transcription	Primary B cells from cord blood	blood
4	chr15:76585200-76602400	Weak transcription	Primary T cells from cord blood	blood
5	chr15:76586200-76602400	Weak transcription	NH-A	brain
6	chr15:76586400-76602400	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:76592600-76602400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:76593400-76602400	Weak transcription	Lung	lung
9	chr15:76593400-76602600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:76597000-76602600	Weak transcription	Fetal Intestine Small	intestine
11	chr15:76599400-76602800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:76599800-76602400	Weak transcription	Fetal Brain Female	brain
13	chr15:76600800-76602800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:76601000-76602800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:76601200-76602600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:76601200-76602800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr15:76601400-76602400	Enhancers	Right Atrium	heart
18	chr15:76601400-76602800	Enhancers	Placenta	Placenta
19	chr15:76601600-76603000	Weak transcription	Gastric	stomach
20	chr15:76601800-76602400	Active TSS	GM12878-XiMat	blood
21	chr15:76601800-76602400	Enhancers	HUVEC	blood vessel
22	chr15:76601800-76602400	Enhancers	NHDF-Ad	bronchial
23	chr15:76601800-76602600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr15:76601800-76602800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:76601800-76602800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:76601800-76602800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr15:76601800-76602800	Flanking Active TSS	HepG2	liver
28	chr15:76601800-76603000	Flanking Active TSS	Hela-S3	cervix
29	chr15:76602000-76602400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:76602000-76602400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr15:76602000-76602400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:76602000-76602400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:76602000-76602400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr15:76602000-76602400	Enhancers	Fetal Intestine Large	intestine
35	chr15:76602000-76602400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr15:76602000-76602400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr15:76602000-76602400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr15:76602000-76602400	Enhancers	HSMM	muscle
39	chr15:76602000-76602400	Enhancers	Osteobl	bone
40	chr15:76602000-76602600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:76602000-76602600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:76602000-76602600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr15:76602000-76602600	Enhancers	Fetal Brain Male	brain
44	chr15:76602000-76602600	Enhancers	Fetal Lung	lung
45	chr15:76602000-76602600	Enhancers	Right Ventricle	heart
46	chr15:76602000-76602600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr15:76602000-76602800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr15:76602000-76602800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr15:76602000-76602800	Enhancers	Primary B cells from peripheral blood	blood
50	chr15:76602000-76602800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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