Variant report

Variant	rs3764396
Chromosome Location	chr17:46015969-46015970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46014365..46016390-chr17:46047533..46049102,2	MCF-7	breast:
2	chr17:45920681..45922665-chr17:46015895..46018695,2	K562	blood:
3	chr17:46014622..46017443-chr17:46017878..46019872,2	MCF-7	breast:
4	chr17:45978248..45980745-chr17:46013180..46016044,2	K562	blood:
5	chr17:46015450..46017408-chr17:46022063..46023841,2	K562	blood:
6	chr17:45886985..45889138-chr17:46015655..46018408,2	K562	blood:

Variant related genes	Relation type
ENSG00000234494	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000108439	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10459927	0.82[ASN][1000 genomes]
rs11079801	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079803	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108833	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1130932	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[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];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652827	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11654010	0.80[JPT][hapmap]
rs11655068	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655352	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11659126	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870852	0.83[ASN][1000 genomes]
rs12601827	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602494	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs12939739	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13353189	0.81[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap]
rs2002136	0.82[CEU][hapmap]
rs2228251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2228253	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2229358	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2318118	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2325747	0.87[ASN][1000 genomes]
rs2325749	0.81[ASN][1000 genomes]
rs2325751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525107	0.83[ASN][1000 genomes]
rs2597169	0.80[MEX][hapmap]
rs2875735	0.80[MEX][hapmap]
rs3096	0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs34593510	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35280206	0.87[ASN][1000 genomes]
rs36124074	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4369725	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793731	0.87[ASN][1000 genomes]
rs4793732	0.84[ASN][1000 genomes]
rs4793733	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4793737	0.87[ASN][1000 genomes]
rs4794261	0.83[ASN][1000 genomes]
rs4794286	0.87[ASN][1000 genomes]
rs4794332	0.87[ASN][1000 genomes]
rs6503934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67194241	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7208707	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7211859	0.90[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7220104	0.82[CEU][hapmap]
rs72840237	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066893	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8071003	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9895863	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9903223	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv2072	chr17:45998637-46019626	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3764396	KAT2A	cis	parietal	SCAN
rs3764396	RP11-6N17.4	cis	Muscle Skeletal	GTEx
rs3764396	SP2	Cis_1M	lymphoblastoid	RTeQTL
rs3764396	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx
rs3764396	SP2	cis	lymphoblastoid	seeQTL
rs3764396	HOXB2	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
2	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
3	chr17:45999200-46018200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:46003200-46018400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:46004600-46018200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr17:46005400-46017400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:46005400-46018200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:46006200-46017800	Weak transcription	Small Intestine	intestine
9	chr17:46007000-46018200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr17:46007000-46018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:46007200-46018200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:46007600-46017400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr17:46007600-46018200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr17:46007600-46018600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:46007800-46018200	Weak transcription	Colonic Mucosa	Colon
16	chr17:46007800-46018400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr17:46007800-46018800	Weak transcription	Gastric	stomach
18	chr17:46008000-46018200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr17:46008000-46018200	Weak transcription	Fetal Intestine Large	intestine
20	chr17:46008000-46018200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr17:46008000-46018400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr17:46008000-46018400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:46008200-46017400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr17:46008200-46017400	Weak transcription	Pancreas	Pancrea
25	chr17:46008200-46017600	Weak transcription	Liver	Liver
26	chr17:46008200-46017600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr17:46008200-46017600	Weak transcription	Ovary	ovary
28	chr17:46008200-46017600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr17:46008200-46018200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr17:46008200-46018200	Weak transcription	Primary B cells from cord blood	blood
31	chr17:46008200-46018200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr17:46008200-46018200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr17:46008200-46018200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:46008200-46018200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr17:46008200-46018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr17:46008200-46018400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:46008200-46018400	Weak transcription	Aorta	Aorta
38	chr17:46008400-46017400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr17:46008400-46017600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr17:46008400-46017600	Weak transcription	Right Ventricle	heart
41	chr17:46008400-46017600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr17:46008400-46018200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr17:46008400-46018400	Weak transcription	Brain Germinal Matrix	brain
44	chr17:46009000-46017600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:46009600-46018200	Weak transcription	Primary T cells from cord blood	blood
46	chr17:46009600-46018200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:46009600-46018400	Weak transcription	Placenta	Placenta
48	chr17:46009800-46017600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:46009800-46018200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:46010400-46018600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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