Variant report

Variant	rs17616799
Chromosome Location	chr17:46039553-46039554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46037386..46040340-chr17:46123583..46126115,2	MCF-7	breast:
2	chr17:46037638..46039949-chr17:46100422..46103113,2	MCF-7	breast:
3	chr17:46025428..46027974-chr17:46037892..46040881,2	K562	blood:
4	chr17:45907437..45910086-chr17:46037370..46039885,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141294	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1133221	0.84[ASW][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.94[MKK][hapmap];0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1473117	0.86[EUR][1000 genomes]
rs16949270	0.84[ASW][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.94[MKK][hapmap];0.91[AFR][1000 genomes]
rs16949296	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs16949427	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs16949651	0.93[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs16951519	0.88[GIH][hapmap]
rs1962201	0.87[ASN][1000 genomes]
rs1986694	0.85[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs208008	0.88[GIH][hapmap]
rs208009	0.88[GIH][hapmap]
rs2240119	0.94[GIH][hapmap]
rs2240120	0.88[GIH][hapmap]
rs2240121	0.88[GIH][hapmap]
rs2285860	0.94[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2325750	0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2525105	0.86[CEU][hapmap];0.93[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55982711	0.91[EUR][1000 genomes]
rs56006220	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs56402159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57782323	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58848175	0.97[ASN][1000 genomes]
rs61396871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72823519	0.91[EUR][1000 genomes]
rs757353	0.94[GIH][hapmap]
rs8071199	0.88[GIH][hapmap]
rs8071879	0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17616799	SNX11	cis	multi-tissue	Pritchard
rs17616799	HOXB2	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
2	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
3	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
4	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46030200-46045800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr17:46035000-46047400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr17:46036000-46047200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr17:46036200-46043400	Weak transcription	A549	lung
11	chr17:46036600-46047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:46036800-46047400	Weak transcription	Thymus	Thymus
13	chr17:46037800-46042400	Weak transcription	Placenta	Placenta
14	chr17:46037800-46047400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:46037800-46047400	Enhancers	Fetal Intestine Small	intestine
16	chr17:46037800-46047800	Enhancers	Fetal Intestine Large	intestine
17	chr17:46038000-46040600	Enhancers	Stomach Mucosa	stomach
18	chr17:46038000-46043000	Weak transcription	Esophagus	oesophagus
19	chr17:46038000-46043800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr17:46038000-46046400	Weak transcription	K562	blood
21	chr17:46038400-46040800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr17:46038400-46042400	Weak transcription	HepG2	liver
23	chr17:46038600-46043400	Enhancers	Colonic Mucosa	Colon
24	chr17:46039000-46039600	Strong transcription	Primary T cells from cord blood	blood
25	chr17:46039000-46040000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr17:46039200-46042800	Weak transcription	Gastric	stomach
27	chr17:46039200-46043000	Weak transcription	Pancreas	Pancrea
28	chr17:46039400-46041600	Weak transcription	Small Intestine	intestine
29	chr17:46039400-46042400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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