Variant report

Variant	rs17139661
Chromosome Location	chr5:115723127-115723128
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10035646	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10036292	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10040345	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10042278	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10043228	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10051240	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10155600	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs10519448	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12152964	1.00[CEU][hapmap]
rs12153717	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12332658	1.00[JPT][hapmap]
rs12514110	0.83[AMR][1000 genomes]
rs12515251	1.00[JPT][hapmap]
rs12515466	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12519989	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12520568	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12520613	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12521612	1.00[JPT][hapmap]
rs12522441	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12523347	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs13362043	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17139192	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17139193	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17139224	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17139265	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17139457	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6880880	1.00[JPT][hapmap]
rs7703121	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7727882	0.85[CEU][hapmap];1.00[JPT][hapmap]

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	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	esv2763489	chr5:115693166-115733327	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17139661	GALNT9	trans	lymphoblastoid	seeQTL
rs17139661	COMMD10	cis	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115697600-115748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:115706000-115724400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:115706800-115723200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:115707600-115748400	Weak transcription	Fetal Intestine Large	intestine
5	chr5:115708600-115754000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:115711800-115730600	Weak transcription	Gastric	stomach
7	chr5:115714400-115724400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:115714400-115730200	Weak transcription	Right Ventricle	heart
9	chr5:115714600-115724200	Weak transcription	Psoas Muscle	Psoas
10	chr5:115715600-115724400	Weak transcription	Fetal Kidney	kidney
11	chr5:115717800-115724200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:115717800-115724200	Weak transcription	Left Ventricle	heart
13	chr5:115717800-115724200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:115717800-115724400	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:115718200-115723200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:115718200-115724400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:115718200-115724600	Weak transcription	Fetal Brain Female	brain
18	chr5:115718400-115737000	Weak transcription	Primary B cells from cord blood	blood
19	chr5:115718600-115748400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:115718800-115724400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:115718800-115731000	Weak transcription	Spleen	Spleen
22	chr5:115719000-115724400	Weak transcription	Adipose Nuclei	Adipose
23	chr5:115719000-115724400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:115719400-115724400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:115719400-115734800	Weak transcription	Primary T cells from cord blood	blood
26	chr5:115719600-115728000	Weak transcription	Fetal Intestine Small	intestine
27	chr5:115722200-115724400	Weak transcription	Esophagus	oesophagus
28	chr5:115722800-115723400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:115722800-115723400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr5:115723000-115724200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:115723000-115724200	Weak transcription	HUVEC	blood vessel
32	chr5:115723000-115724400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:115723000-115724400	Weak transcription	Pancreas	Pancrea
34	chr5:115723000-115776000	Weak transcription	Primary hematopoietic stem cells	blood

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