Variant report

Variant	rs10832918
Chromosome Location	chr11:18335684-18335685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10766469	0.80[EUR][1000 genomes]
rs10766471	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10832919	0.81[EUR][1000 genomes]
rs10832920	0.91[CEU][hapmap]
rs11024605	0.83[JPT][hapmap]
rs11024607	0.83[JPT][hapmap]
rs11024608	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024609	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11024612	0.83[JPT][hapmap]
rs11024613	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11024614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024619	0.80[ASN][1000 genomes]
rs11024621	0.83[JPT][hapmap]
rs11024622	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12224608	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs12294486	0.80[EUR][1000 genomes]
rs2037867	0.90[CEU][hapmap]
rs2305564	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2305565	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2403254	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs3781944	0.83[JPT][hapmap]
rs3802967	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs4150581	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs4150606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4150644	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4366463	0.82[JPT][hapmap]
rs4586132	0.83[JPT][hapmap]
rs4596	0.92[CEU][hapmap]
rs4757638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7113249	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7122032	0.83[JPT][hapmap]
rs7128017	0.83[JPT][hapmap]
rs7128146	0.83[JPT][hapmap]
rs7478729	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10832918	HPS5	cis	cerebellum	SCAN
rs10832918	HPS5	cis	parietal	SCAN
rs10832918	GTF2H1	cis	multi-tissue	Pritchard
rs10832918	GTF2H1	cis	Esophagus Mucosa	GTEx
rs10832918	LDHAL6A	cis	cerebellum	SCAN
rs10832918	GTF2H1	cis	parietal	SCAN
rs10832918	LDHA	cis	parietal	SCAN
rs10832918	GTF2H1	cis	cerebellum	SCAN
rs10832918	PIK3C2A	cis	cerebellum	SCAN
rs10832918	MRGPRX2	cis	cerebellum	SCAN
rs10832918	SAA2	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18300200-18336000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr11:18311800-18343000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:18317200-18342200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:18320600-18337400	Weak transcription	Gastric	stomach
5	chr11:18327800-18342200	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:18327800-18342200	Weak transcription	HUVEC	blood vessel
7	chr11:18330200-18340000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:18330200-18340800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:18331000-18341000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:18331000-18341600	Weak transcription	Fetal Lung	lung
11	chr11:18331000-18342200	Weak transcription	Right Ventricle	heart
12	chr11:18331600-18341600	Weak transcription	Psoas Muscle	Psoas
13	chr11:18331800-18336600	Weak transcription	Spleen	Spleen
14	chr11:18332000-18341800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:18332200-18335800	Enhancers	HMEC	breast
16	chr11:18332200-18336400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:18332200-18342200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:18332400-18336200	Weak transcription	Left Ventricle	heart
19	chr11:18332600-18335800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr11:18332600-18337400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:18332600-18340000	Weak transcription	Liver	Liver
22	chr11:18332600-18341000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:18332600-18342800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:18332600-18342800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr11:18332600-18343000	Weak transcription	Lung	lung
26	chr11:18332800-18337400	Weak transcription	Fetal Brain Female	brain
27	chr11:18332800-18340800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr11:18332800-18341000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:18332800-18341800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr11:18332800-18341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:18332800-18342200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:18332800-18342200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr11:18332800-18342800	Weak transcription	Fetal Brain Male	brain
34	chr11:18333000-18336000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr11:18333000-18336600	Enhancers	HSMMtube	muscle
36	chr11:18333000-18338200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:18333000-18341600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr11:18333000-18341800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:18333000-18341800	Weak transcription	Thymus	Thymus
40	chr11:18333000-18342000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:18333000-18342000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:18333000-18342000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr11:18333000-18342200	Weak transcription	Adipose Nuclei	Adipose
44	chr11:18333000-18342400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr11:18333000-18342400	Weak transcription	Colonic Mucosa	Colon
46	chr11:18333000-18342800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr11:18333000-18342800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr11:18333200-18342200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr11:18333400-18335800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:18333400-18335800	Enhancers	Ovary	ovary

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