Variant report

Variant	rs17086746
Chromosome Location	chr4:57259999-57260000
allele	C/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	CTCF	chr4:57259941-57260012	Lung_OC	lung:	n/a	n/a
2	POLR2A	chr4:57259888-57260136	K562	blood:	n/a	n/a
3	POLR2A	chr4:57259942-57260014	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr4:57259915-57260079	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57252534..57255192-chr4:57257421..57260881,3	MCF-7	breast:
2	chr4:57257925..57261959-chr4:57299598..57302953,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270147	TF binding region
ENSG00000269921	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000157426	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1401908	0.92[JPT][hapmap]
rs17086755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086769	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17086776	0.92[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17086786	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17086844	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17086879	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17086893	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17086906	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17086908	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17086924	1.00[EUR][1000 genomes]
rs2292984	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28649329	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34228795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34543011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796543	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][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];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4074775	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41476944	0.92[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57439970	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58337902	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59161426	0.82[ASN][1000 genomes]
rs61580407	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61732641	1.00[EUR][1000 genomes]
rs73155895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73157733	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73157739	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73157754	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73157769	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73157772	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73157774	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73157784	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73159959	0.81[ASN][1000 genomes]
rs73159992	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73162272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73167378	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73167396	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7437329	0.92[JPT][hapmap]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh 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	88 gene(s)	inside rSNPs	diseases
5	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17086746	ARL9	cis	multi-tissue	Pritchard
rs17086746	ARL9	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57268400	Weak transcription	Lung	lung
3	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
4	chr4:57254600-57264000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:57254600-57271600	Weak transcription	Ovary	ovary
6	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
7	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:57254800-57260800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:57254800-57261800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:57254800-57262000	Weak transcription	Placenta	Placenta
11	chr4:57254800-57264000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:57254800-57264000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:57254800-57271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
19	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
20	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:57255000-57260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:57255000-57261200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:57255000-57262200	Weak transcription	A549	lung
24	chr4:57255000-57264400	Weak transcription	Brain Germinal Matrix	brain
25	chr4:57255000-57264800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:57255000-57265600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:57255000-57266000	Weak transcription	Primary B cells from cord blood	blood
28	chr4:57255000-57266200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:57255000-57266200	Weak transcription	NH-A	brain
30	chr4:57255000-57266400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr4:57255000-57266400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:57255000-57266600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:57255000-57266600	Weak transcription	HSMM	muscle
34	chr4:57255000-57266800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:57255000-57269200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:57255000-57271400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:57255200-57262000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:57255200-57262200	Weak transcription	Fetal Lung	lung
39	chr4:57255200-57262200	Weak transcription	Osteobl	bone
40	chr4:57255200-57264000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:57255200-57264000	Weak transcription	Fetal Stomach	stomach
42	chr4:57255200-57266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:57255200-57266200	Weak transcription	HUVEC	blood vessel
44	chr4:57255200-57266400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr4:57255200-57266800	Weak transcription	Fetal Kidney	kidney
46	chr4:57255200-57266800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:57255200-57267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:57255200-57267400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:57255200-57271600	Weak transcription	NHEK	skin
50	chr4:57255200-57272200	Weak transcription	Stomach Smooth Muscle	stomach

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