Variant report

Variant	rs3796473
Chromosome Location	chr4:76593995-76593996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76592494..76594914-chr4:76648376..76650712,2	K562	blood:
2	chr4:76588364..76594216-chr4:76595418..76601309,9	MCF-7	breast:
3	chr4:76593006..76595820-chr4:76737546..76740383,2	K562	blood:
4	chr4:76574757..76576381-chr4:76592960..76594947,2	K562	blood:

Variant related genes	Relation type
ENSG00000138757	Chromatin interaction
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10014281	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10025315	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10028884	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10029110	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11097069	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11097070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11729258	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11736474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737705	0.86[EUR][1000 genomes]
rs13116639	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13118426	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13133699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13137468	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138717	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13140908	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1464070	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1464071	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546539	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1548175	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1553986	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1828629	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1913299	0.80[AMR][1000 genomes]
rs1967495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226416	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2280095	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs324685	0.82[AMR][1000 genomes]
rs324689	0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324692	0.80[EUR][1000 genomes]
rs324695	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs324707	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324708	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324711	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324715	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324716	0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324717	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324718	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324721	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324724	0.80[EUR][1000 genomes]
rs324725	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[EUR][1000 genomes]
rs324737	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3796485	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796488	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3853183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3853184	0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3942252	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4337757	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4349625	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs436611	0.82[EUR][1000 genomes]
rs443952	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4859403	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859537	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs4859542	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859544	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859545	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859546	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859547	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859550	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5020591	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6419115	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6531778	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6531841	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531866	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531867	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531868	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531889	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6531902	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6531903	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6826858	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6827809	1.00[CHB][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6828365	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6829402	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6832912	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6835702	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835819	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6842216	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6855321	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6858530	0.80[AFR][1000 genomes]
rs6858741	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7356270	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7356310	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7657871	0.85[EUR][1000 genomes]
rs7659408	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7662940	1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7672378	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674063	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7674328	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677150	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7685459	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7691385	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7691765	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7696241	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9942164	0.95[AMR][1000 genomes];0.83[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	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3796473	PPEF2	cis	parietal	SCAN
rs3796473	MEA1	trans	brain	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76566200-76596600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:76567400-76596600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:76572000-76594400	Weak transcription	Aorta	Aorta
4	chr4:76573800-76596200	Weak transcription	Colonic Mucosa	Colon
5	chr4:76574000-76596400	Weak transcription	Right Ventricle	heart
6	chr4:76578000-76596400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:76578000-76597000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:76578000-76597000	Weak transcription	Esophagus	oesophagus
9	chr4:76579000-76594000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:76581000-76594000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:76583400-76595800	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:76583400-76595800	Weak transcription	Fetal Kidney	kidney
13	chr4:76583400-76596200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:76583400-76596200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:76583600-76594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:76583600-76594200	Weak transcription	Adipose Nuclei	Adipose
17	chr4:76583600-76596200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:76583800-76596200	Weak transcription	Brain Substantia Nigra	brain
19	chr4:76584400-76594000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:76584400-76596000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:76584400-76596200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:76584400-76596600	Weak transcription	HSMMtube	muscle
23	chr4:76584600-76596400	Weak transcription	Brain Angular Gyrus	brain
24	chr4:76584600-76597200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:76585200-76596000	Weak transcription	NHLF	lung
26	chr4:76586400-76594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:76586600-76597400	Weak transcription	Gastric	stomach
28	chr4:76586800-76596000	Weak transcription	Fetal Lung	lung
29	chr4:76586800-76596400	Weak transcription	HSMM	muscle
30	chr4:76586800-76597000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:76586800-76597200	Weak transcription	Lung	lung
32	chr4:76587000-76595200	Weak transcription	Brain Anterior Caudate	brain
33	chr4:76587000-76597000	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:76587200-76596000	Weak transcription	Fetal Stomach	stomach
35	chr4:76587200-76596400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:76587200-76596400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:76587400-76595000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:76587400-76595600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:76587400-76595600	Weak transcription	Fetal Brain Female	brain
40	chr4:76587400-76597000	Weak transcription	Placenta	Placenta
41	chr4:76588000-76595600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:76588000-76596200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:76588000-76596200	Weak transcription	HMEC	breast
44	chr4:76588000-76596400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:76588200-76594200	Weak transcription	A549	lung
46	chr4:76588200-76596000	Weak transcription	Osteobl	bone
47	chr4:76588200-76596200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr4:76588400-76595400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:76588600-76594000	Weak transcription	Thymus	Thymus
50	chr4:76588600-76594400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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