Variant report

Variant	rs335697
Chromosome Location	chr15:76210367-76210368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76196151..76197673-chr15:76207944..76210388,2	K562	blood:
2	chr15:76196519..76198808-chr15:76210180..76211825,2	MCF-7	breast:
3	chr15:76198411..76200374-chr15:76209786..76212677,2	K562	blood:

Variant related genes	Relation type
ENSG00000167196	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12910576	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12915012	0.87[AMR][1000 genomes]
rs1391894	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap]
rs1695378	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699263	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184580	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs189197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441929	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2455899	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[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];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2460800	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469039	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2593277	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2593278	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[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];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28876229	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2955733	0.92[GIH][hapmap]
rs2959842	0.92[GIH][hapmap]
rs2959852	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs334930	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs334934	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs334936	0.81[AMR][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];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs335706	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[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];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[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];0.91[AMR][1000 genomes];0.83[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];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4886754	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71403522	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024155	0.95[AMR][1000 genomes];0.91[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];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1040053	chr15:76197988-76314542	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs335697	NRG4	cis	cerebellum	SCAN
rs335697	NRG4	cis	parietal	SCAN
rs335697	LRRC49	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76197000-76210800	Weak transcription	Aorta	Aorta
2	chr15:76197000-76214600	Weak transcription	Small Intestine	intestine
3	chr15:76197200-76216800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:76197200-76216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:76197800-76214400	Weak transcription	Stomach Mucosa	stomach
6	chr15:76197800-76217400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:76198000-76214400	Weak transcription	Esophagus	oesophagus
8	chr15:76198000-76214400	Weak transcription	Pancreas	Pancrea
9	chr15:76198000-76214600	Weak transcription	Right Ventricle	heart
10	chr15:76198000-76231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:76198200-76232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:76198400-76214200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:76198400-76225000	Weak transcription	Fetal Kidney	kidney
14	chr15:76198600-76217000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:76198600-76226400	Weak transcription	Fetal Brain Male	brain
16	chr15:76199000-76215800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:76199200-76212000	Weak transcription	Psoas Muscle	Psoas
18	chr15:76201200-76214400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:76203800-76230200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:76205200-76211000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:76205200-76213200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:76205400-76212000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:76205400-76212200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:76205400-76213000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:76205400-76213400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:76205400-76213600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:76205400-76213600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:76205400-76213600	Strong transcription	A549	lung
29	chr15:76205400-76213800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:76205400-76214200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:76205400-76215400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:76205400-76217200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:76205400-76217200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr15:76205400-76218600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:76205600-76211400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:76205600-76213000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:76205600-76213000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:76205600-76216200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:76205600-76216400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr15:76205800-76210600	Strong transcription	HepG2	liver
41	chr15:76205800-76216800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:76206000-76212800	Strong transcription	Adipose Nuclei	Adipose
43	chr15:76206400-76210800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr15:76206400-76213400	Strong transcription	NHEK	skin
45	chr15:76206800-76211800	Weak transcription	Fetal Thymus	thymus
46	chr15:76206800-76218800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr15:76207000-76226600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:76207000-76228200	Weak transcription	Brain Substantia Nigra	brain
49	chr15:76207000-76228200	Weak transcription	Colonic Mucosa	Colon
50	chr15:76207000-76232000	Weak transcription	Rectal Smooth Muscle	rectum

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