Variant report

Variant	rs17216446
Chromosome Location	chr4:99976646-99976647
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99848990..99851427-chr4:99975088..99976900,2	K562	blood:
2	chr4:99180664..99184251-chr4:99975282..99978632,3	MCF-7	breast:
3	chr4:99972162..99974630-chr4:99975486..99978459,2	MCF-7	breast:
4	chr4:99970407..99973729-chr4:99975886..99978831,3	K562	blood:
5	chr4:99974718..99976899-chr4:99981124..99982868,2	MCF-7	breast:
6	chr4:99843188..99846109-chr4:99975647..99978634,2	K562	blood:
7	chr4:99975077..99977484-chr4:100009291..100011650,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246090	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000138698	Chromatin interaction
ENSG00000214559	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000197894	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10014193	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10016255	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10023577	0.85[CEU][hapmap]
rs10035037	0.85[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1037475	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10433890	0.85[CEU][hapmap]
rs11097643	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097645	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721765	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11723037	0.85[CEU][hapmap]
rs11725932	0.81[CEU][hapmap]
rs11730116	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11731878	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11944824	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1230159	0.92[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs1230160	0.91[ASN][1000 genomes]
rs1230169	0.91[ASN][1000 genomes]
rs1230174	0.86[ASN][1000 genomes]
rs1230175	0.91[CHB][hapmap];0.91[ASN][1000 genomes]
rs1230178	0.92[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs1230179	0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs1230182	0.92[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs1230186	0.92[CHB][hapmap];0.93[CHD][hapmap];0.91[ASN][1000 genomes]
rs1230188	0.86[YRI][hapmap]
rs1230190	0.86[YRI][hapmap]
rs1230195	0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs1230196	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs1230197	0.91[ASN][1000 genomes]
rs1230200	0.91[ASN][1000 genomes]
rs1230203	0.91[ASN][1000 genomes]
rs1230205	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[ASN][1000 genomes]
rs1230206	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[ASN][1000 genomes]
rs1230207	0.95[ASN][1000 genomes]
rs1230209	0.92[CHB][hapmap];0.90[ASN][1000 genomes]
rs1234973	0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs12374261	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1238741	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[ASN][1000 genomes]
rs12498533	0.84[CEU][hapmap]
rs12512420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644580	0.85[CEU][hapmap]
rs1453869	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1453871	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1584838	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17028293	0.81[CEU][hapmap]
rs1869459	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2123782	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2167981	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602910	0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs28539514	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2866032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35203362	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3974876	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4699693	0.85[CEU][hapmap]
rs57098596	0.95[ASN][1000 genomes]
rs62323229	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6810489	0.81[CEU][hapmap]
rs6817991	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6822589	0.85[CEU][hapmap]
rs6830125	0.84[CEU][hapmap]
rs6840282	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6840922	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6846221	0.96[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6848246	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6850128	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6850293	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6852715	0.85[CEU][hapmap]
rs6854386	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7656935	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7674742	0.96[CEU][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7676259	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7690818	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9685062	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9992105	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17216446	ADH5	cis	cerebellum	SCAN
rs17216446	CENPE	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99944200-99979000	Weak transcription	Colonic Mucosa	Colon
2	chr4:99944200-99979200	Weak transcription	Right Ventricle	heart
3	chr4:99944400-99979200	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:99946000-99976800	Weak transcription	Stomach Mucosa	stomach
5	chr4:99946200-99977000	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:99946400-99979000	Weak transcription	Esophagus	oesophagus
7	chr4:99947000-99979000	Weak transcription	Gastric	stomach
8	chr4:99947000-99979200	Weak transcription	Pancreas	Pancrea
9	chr4:99947400-99982600	Weak transcription	Psoas Muscle	Psoas
10	chr4:99949000-99979000	Weak transcription	Small Intestine	intestine
11	chr4:99954000-99999200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:99954800-99977000	Weak transcription	Brain Substantia Nigra	brain
13	chr4:99955400-99980800	Weak transcription	HSMMtube	muscle
14	chr4:99956200-99995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:99959800-100000200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:99964200-99979000	Weak transcription	Brain Germinal Matrix	brain
17	chr4:99965000-99982000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:99965000-99982200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:99965600-99976800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:99965600-99976800	Strong transcription	Fetal Thymus	thymus
21	chr4:99965600-99977000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:99965600-99977200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:99966600-99977000	Weak transcription	HUVEC	blood vessel
24	chr4:99968600-99977000	Weak transcription	Brain Angular Gyrus	brain
25	chr4:99969000-99977000	Weak transcription	Fetal Heart	heart
26	chr4:99969200-99979200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:99969600-99976800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:99970400-99977000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:99970400-99977000	Weak transcription	HepG2	liver
30	chr4:99970600-99976800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:99970600-99977200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:99971000-99976800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:99971000-99988800	Weak transcription	Fetal Brain Male	brain
34	chr4:99971200-99976800	Weak transcription	NH-A	brain
35	chr4:99971400-99976800	Weak transcription	A549	lung
36	chr4:99971800-99976800	Weak transcription	NHLF	lung
37	chr4:99971800-99991600	Weak transcription	Brain Anterior Caudate	brain
38	chr4:99971800-99997600	Weak transcription	Spleen	Spleen
39	chr4:99972000-99976800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:99972000-99976800	Weak transcription	K562	blood
41	chr4:99972000-99979200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:99972000-99982400	Weak transcription	Lung	lung
43	chr4:99972400-99978400	Weak transcription	Placenta	Placenta
44	chr4:99972400-99978600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:99972400-99979200	Weak transcription	Ovary	ovary
46	chr4:99972600-99976800	Weak transcription	NHEK	skin
47	chr4:99973400-99978200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:99973600-99977000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:99973800-99977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:99973800-99978200	Weak transcription	Primary T cells fromperipheralblood	blood

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