Variant report

Variant	rs2255701
Chromosome Location	chr15:76196709-76196710
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:76195569..76197871-chr15:76205442..76207733,2	K562	blood:
2	chr15:76196519..76198808-chr15:76210180..76211825,2	MCF-7	breast:
3	chr15:76135493..76137289-chr15:76195431..76198634,3	MCF-7	breast:
4	chr15:76195569..76197871-chr15:76204617..76208764,4	K562	blood:
5	chr15:38544112..38545065-chr15:76195734..76196719,2	Hela-S3	cervix:
6	chr15:76134186..76138083-chr15:76192925..76200499,13	K562	blood:
7	chr15:76194745..76198135-chr15:76223912..76227637,3	MCF-7	breast:
8	chr13:28194510..28195037-chr15:76196289..76196837,2	Hela-S3	cervix:
9	chr15:76133681..76139746-chr15:76193985..76199740,23	MCF-7	breast:
10	chr15:76135754..76137278-chr15:76196181..76197882,2	K562	blood:
11	chr15:76195094..76197177-chr15:76350015..76352498,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000186184	Chromatin interaction
ENSG00000140367	Chromatin interaction
ENSG00000166068	Chromatin interaction
ENSG00000169758	Chromatin interaction
ENSG00000167196	Chromatin interaction
ENSG00000139517	Chromatin interaction
ENSG00000169752	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12910576	0.86[AMR][1000 genomes]
rs12915012	0.83[AMR][1000 genomes]
rs1391894	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs1695378	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699263	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184580	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs189197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2441929	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2455899	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460798	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2460800	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469039	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2593277	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2593278	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593280	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28876229	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2955733	0.92[GIH][hapmap]
rs2959842	0.92[GIH][hapmap]
rs2959852	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs334930	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs334934	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs335681	0.93[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs335697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335706	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886747	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886753	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886754	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71403522	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024155	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs985849	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[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	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1044733	chr15:76120924-76228880	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1053717	chr15:76196674-76314542	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2255701	NRG4	cis	cerebellum	SCAN
rs2255701	LRRC49	cis	cerebellum	SCAN
rs2255701	NRG4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76194800-76197200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr15:76195200-76196800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:76195200-76196800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:76195200-76197200	Active TSS	Brain Anterior Caudate	brain
5	chr15:76195400-76196800	Active TSS	Duodenum Mucosa	Duodenum
6	chr15:76195400-76197000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr15:76195400-76197200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:76195400-76197200	Active TSS	Fetal Kidney	kidney
9	chr15:76195400-76197200	Active TSS	NHLF	lung
10	chr15:76195400-76197400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr15:76195400-76197400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr15:76195400-76197400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr15:76195400-76197400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:76195400-76197400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr15:76195400-76197600	Active TSS	H9 Cell Line	embryonic stem cell
16	chr15:76195600-76196800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:76195600-76196800	Active TSS	Colonic Mucosa	Colon
18	chr15:76195600-76196800	Active TSS	Fetal Brain Male	brain
19	chr15:76195600-76196800	Active TSS	Left Ventricle	heart
20	chr15:76195600-76196800	Active TSS	Psoas Muscle	Psoas
21	chr15:76195600-76197000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:76195600-76197000	Active TSS	Lung	lung
23	chr15:76195600-76197000	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr15:76195600-76197200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:76195600-76197200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:76195600-76197200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:76195600-76197200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr15:76195600-76197200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:76195600-76197200	Active TSS	Fetal Intestine Small	intestine
30	chr15:76195600-76197200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr15:76195600-76197200	Active TSS	Fetal Lung	lung
32	chr15:76195600-76197200	Active TSS	Ovary	ovary
33	chr15:76195600-76197200	Active TSS	Right Atrium	heart
34	chr15:76195600-76197400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:76195600-76197400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:76195600-76197400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr15:76195600-76197400	Active TSS	Fetal Brain Female	brain
38	chr15:76195600-76197600	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr15:76195600-76197600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:76195600-76197600	Active TSS	Stomach Smooth Muscle	stomach
41	chr15:76195800-76196800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:76195800-76196800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr15:76195800-76196800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr15:76195800-76196800	Active TSS	Brain Substantia Nigra	brain
45	chr15:76195800-76196800	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr15:76195800-76196800	Active TSS	Right Ventricle	heart
47	chr15:76195800-76197000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:76195800-76197000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:76195800-76197000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:76195800-76197000	Active TSS	Aorta	Aorta

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