Variant report

Variant	rs335711
Chromosome Location	chr15:76184740-76184741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr15:76183902-76185223	IMR90	lung:	n/a	n/a
2	TCF12	chr15:76184005-76184817	SK-N-SH	brain:	n/a	chr15:76184320-76184330
3	TCF12	chr15:76184126-76184805	SK-N-SH	brain:	n/a	chr15:76184320-76184330
4	GATA3	chr15:76184186-76184832	SK-N-SH	brain:	n/a	chr15:76184413-76184423
5	GATA3	chr15:76184017-76184818	SK-N-SH	brain:	n/a	chr15:76184413-76184423

No.	Distal block	Cell Line	Cell type
1	chr15:76135763..76139600-chr15:76181865..76185802,4	MCF-7	breast:
2	chr15:76182009..76185203-chr15:76186533..76188570,4	K562	blood:
3	chr15:76173887..76175756-chr15:76183628..76185544,2	K562	blood:
4	chr15:76177375..76179318-chr15:76182768..76185723,2	MCF-7	breast:
5	chr15:76119180..76121817-chr15:76184055..76185596,2	K562	blood:
6	chr15:76184501..76187276-chr15:76194759..76196406,2	MCF-7	breast:
7	chr15:76172673..76175756-chr15:76183628..76185667,3	K562	blood:

Variant related genes	Relation type
RN7SL510P	TF binding region
ENSG00000140367	Chromatin interaction
ENSG00000167196	Chromatin interaction
ENSG00000266308	Chromatin interaction

Extended variants
information (count: 33 )
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	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1699263	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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];0.99[ASN][1000 genomes]
rs2255701	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]
rs2441929	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2455899	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460800	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593278	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[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];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs335706	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.94[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	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs335711	NRG4	cis	cerebellum	SCAN
rs335711	LRRC49	cis	cerebellum	SCAN
rs335711	NRG4	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76137800-76188400	Weak transcription	Brain Anterior Caudate	brain
2	chr15:76138200-76195200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:76138200-76195400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:76141400-76195200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:76145200-76195200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:76149000-76195600	Weak transcription	Colonic Mucosa	Colon
7	chr15:76152800-76193400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:76159800-76195400	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:76165400-76188800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:76165600-76185800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:76165600-76194800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:76165800-76186600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:76166200-76186600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:76166400-76193600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:76166400-76194600	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:76166400-76195200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:76166400-76195400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:76166400-76195800	Weak transcription	Gastric	stomach
19	chr15:76166600-76194400	Weak transcription	Right Ventricle	heart
20	chr15:76166600-76195200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:76166600-76195400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:76166600-76195800	Weak transcription	Aorta	Aorta
23	chr15:76166800-76195400	Weak transcription	Fetal Intestine Small	intestine
24	chr15:76167000-76194400	Weak transcription	Spleen	Spleen
25	chr15:76167000-76195600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:76167000-76195800	Weak transcription	Esophagus	oesophagus
27	chr15:76167200-76184800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:76167200-76193800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:76167200-76195200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:76167200-76195600	Weak transcription	Lung	lung
31	chr15:76167600-76195400	Weak transcription	Brain Angular Gyrus	brain
32	chr15:76168000-76185800	Weak transcription	Fetal Lung	lung
33	chr15:76168200-76195000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr15:76172000-76195200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:76172200-76189800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:76172200-76192400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:76172200-76194600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:76172200-76195600	Weak transcription	Fetal Intestine Large	intestine
39	chr15:76172400-76188200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:76172400-76193000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr15:76172400-76193600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:76172400-76193600	Weak transcription	Brain Germinal Matrix	brain
43	chr15:76172400-76195200	Weak transcription	Left Ventricle	heart
44	chr15:76172400-76195600	Weak transcription	Ovary	ovary
45	chr15:76173400-76188600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:76173800-76185200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr15:76176000-76186000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:76176600-76195400	Weak transcription	Fetal Brain Male	brain
49	chr15:76177000-76195200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr15:76177800-76184800	Weak transcription	Fetal Stomach	stomach

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