Variant report

Variant	rs3096
Chromosome Location	chr17:46029432-46029433
allele	G/T
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	MYBL2	chr17:46029378-46030092	HepG2	liver:	n/a	n/a
2	HNF4G	chr17:46029420-46029998	HepG2	liver:	n/a	chr17:46029732-46029747
3	MAX	chr17:46029397-46030197	HepG2	liver:	n/a	n/a
4	POLR2A	chr17:46028862-46030149	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46028612..46030985-chr17:46062999..46064940,2	MCF-7	breast:
2	chr17:46027611..46030432-chr17:46048552..46050466,2	K562	blood:
3	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
4	chr17:46029177..46031751-chr17:46099712..46102366,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264019	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11079801	0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11079803	0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11079804	0.80[MKK][hapmap]
rs1108833	0.83[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs1130932	0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs11545723	0.83[CHB][hapmap];0.80[MKK][hapmap]
rs11652185	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11652827	0.85[ASN][1000 genomes]
rs11654010	0.83[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs11655068	0.87[ASN][1000 genomes]
rs11655352	0.87[ASN][1000 genomes]
rs11659126	0.85[ASN][1000 genomes]
rs12601827	0.87[ASN][1000 genomes]
rs12602494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939739	0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs13353189	0.80[JPT][hapmap]
rs17617250	0.81[CHB][hapmap]
rs2228251	0.85[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs2228253	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2229358	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs2318118	0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2325749	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2325751	0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2525107	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34593510	0.85[ASN][1000 genomes]
rs35280206	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36124074	0.85[ASN][1000 genomes]
rs3764396	0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4369725	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs4793731	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793732	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793734	0.83[CHB][hapmap];0.80[MKK][hapmap]
rs4793737	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794332	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503934	0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs67194241	0.85[ASN][1000 genomes]
rs7208707	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs7211859	0.83[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs757351	0.83[CHB][hapmap]
rs8066893	0.83[ASN][1000 genomes]
rs8071003	0.85[ASN][1000 genomes]
rs9894188	0.82[ASN][1000 genomes]
rs9895863	0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9903223	0.85[ASN][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	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	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3096	PNPO	cis	parietal	SCAN
rs3096	KRT13	cis	parietal	SCAN
rs3096	NFE2L1	cis	parietal	SCAN
rs3096	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs3096	RAB5C	cis	parietal	SCAN
rs3096	RPRML	cis	parietal	SCAN
rs3096	ASB16	cis	parietal	SCAN
rs3096	KRT33A	cis	parietal	SCAN
rs3096	PNPO	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
3	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
5	chr17:46024400-46031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:46027000-46030000	Weak transcription	Psoas Muscle	Psoas
7	chr17:46027200-46030000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:46027200-46031200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr17:46027200-46032600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:46027200-46034400	Weak transcription	Hela-S3	cervix
11	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
12	chr17:46027400-46029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr17:46027400-46029600	Weak transcription	Lung	lung
14	chr17:46027400-46030000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr17:46027400-46030000	Genic enhancers	Stomach Mucosa	stomach
16	chr17:46027400-46030800	Strong transcription	Fetal Stomach	stomach
17	chr17:46027400-46032600	Weak transcription	NHLF	lung
18	chr17:46027400-46033800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr17:46027400-46033800	Weak transcription	NHDF-Ad	bronchial
20	chr17:46027400-46034000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:46027400-46034200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:46027400-46034400	Weak transcription	Fetal Lung	lung
23	chr17:46027400-46034600	Weak transcription	K562	blood
24	chr17:46027400-46034800	Weak transcription	NH-A	brain
25	chr17:46027600-46029800	Genic enhancers	Rectal Mucosa Donor 31	rectum
26	chr17:46027600-46030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:46027600-46030400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:46027600-46030400	Enhancers	Liver	Liver
29	chr17:46027600-46030400	Weak transcription	Brain Substantia Nigra	brain
30	chr17:46027600-46031600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr17:46027600-46032200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr17:46027600-46032600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:46027600-46033000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:46027600-46033800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:46027600-46034200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr17:46027600-46034400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr17:46027600-46034800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
39	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr17:46027800-46029600	Weak transcription	Primary T cells from cord blood	blood
41	chr17:46027800-46029600	Enhancers	HepG2	liver
42	chr17:46027800-46030200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:46027800-46030400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:46027800-46030400	Strong transcription	Osteobl	bone
45	chr17:46027800-46031600	Weak transcription	Small Intestine	intestine
46	chr17:46027800-46032200	Weak transcription	Primary B cells from cord blood	blood
47	chr17:46027800-46032600	Weak transcription	A549	lung
48	chr17:46027800-46032800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr17:46027800-46033600	Weak transcription	Brain Angular Gyrus	brain
50	chr17:46027800-46034000	Weak transcription	Fetal Muscle Trunk	muscle

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