Variant report

Variant	rs11638974
Chromosome Location	chr15:75799306-75799307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75748494..75750085-chr15:75799130..75801162,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10220738	1.00[CEU][hapmap]
rs10851882	0.83[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11072544	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11072552	0.83[GIH][hapmap]
rs1128933	0.83[CHB][hapmap];0.85[GIH][hapmap]
rs11632105	0.83[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs11632813	0.83[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs11634402	0.81[GIH][hapmap]
rs11634863	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636031	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11636199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11637068	0.83[AFR][1000 genomes]
rs11637263	0.81[ASN][1000 genomes]
rs11637586	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11639183	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11855087	0.83[CHB][hapmap]
rs12324230	0.83[CHB][hapmap];0.87[GIH][hapmap]
rs12708518	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12708519	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12708520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12909863	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916256	0.80[ASN][1000 genomes]
rs12916964	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13380103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13737	0.88[CEU][hapmap]
rs28432989	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28610581	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28623700	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28693593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28737338	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28783769	0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs3809547	0.94[CEU][hapmap]
rs3809549	0.83[CHB][hapmap];0.85[GIH][hapmap]
rs4075522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4297648	0.81[ASN][1000 genomes]
rs4299117	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4322627	0.98[GIH][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4381565	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4430707	0.83[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap]
rs4451914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs4462560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4486847	0.81[ASN][1000 genomes]
rs4526985	0.87[GIH][hapmap]
rs4545784	1.00[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4564532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4886443	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap]
rs4886446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4886702	0.83[CHB][hapmap];0.87[GIH][hapmap]
rs4886703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886704	0.83[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs4886705	0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs4886706	0.83[CHB][hapmap]
rs4886707	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4886708	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886712	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4886715	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886716	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs4886718	0.80[GIH][hapmap]
rs4886722	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs60972074	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62027181	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495174	0.83[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs6495176	0.83[CHB][hapmap];0.87[GIH][hapmap]
rs6495181	0.83[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs6495182	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7163451	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7163907	1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs7164541	0.83[CHB][hapmap];0.87[GIH][hapmap]
rs7166281	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs7166737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7175852	1.00[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs7176938	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7180574	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7182283	0.83[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs7184046	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7495610	0.91[EUR][1000 genomes]
rs8023268	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8023815	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8024244	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8027365	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8027546	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8028182	0.87[GIH][hapmap];0.82[TSI][hapmap]
rs8028277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs8029112	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8030802	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8034317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8036758	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8036884	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8038760	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap]
rs9806241	0.83[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs9920028	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs9944207	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	nsv482802	chr15:75686519-75899896	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
8	nsv904387	chr15:75706296-75806911	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	nsv904388	chr15:75730182-75804543	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	nsv904389	chr15:75739824-75806911	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv904390	chr15:75795177-75840943	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11638974	MAN2C1	cis	Nerve Tibial	GTEx
rs11638974	MAN2C1	cis	parietal	SCAN
rs11638974	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs11638974	MAN2C1	cis	Stomach	GTEx
rs11638974	MAN2C1	cis	Heart Left Ventricle	GTEx
rs11638974	MAN2C1	cis	Thyroid	GTEx
rs11638974	MAN2C1	cis	Artery Aorta	GTEx
rs11638974	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs11638974	MAN2C1	cis	Artery Tibial	GTEx
rs11638974	MAN2C1	cis	lung	GTEx
rs11638974	MAN2C1	cis	Esophagus Muscularis	GTEx
rs11638974	MAN2C1	cis	cerebellum	SCAN
rs11638974	MAN2C1	cis	Esophagus Mucosa	GTEx
rs11638974	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs11638974	MAN2C1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75777200-75816800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75777600-75812000	Weak transcription	Small Intestine	intestine
3	chr15:75780200-75812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:75782600-75815200	Weak transcription	K562	blood
5	chr15:75785600-75814200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:75790000-75814200	Weak transcription	Psoas Muscle	Psoas
7	chr15:75797200-75801800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:75797800-75799400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
9	chr15:75797800-75799400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:75797800-75799400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:75797800-75799400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:75797800-75799400	Strong transcription	Liver	Liver
13	chr15:75797800-75799400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:75797800-75799400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr15:75797800-75799400	Strong transcription	Fetal Kidney	kidney
16	chr15:75797800-75799400	Strong transcription	Gastric	stomach
17	chr15:75797800-75799400	Strong transcription	Ovary	ovary
18	chr15:75797800-75799400	Strong transcription	Pancreas	Pancrea
19	chr15:75797800-75799400	Strong transcription	Rectal Smooth Muscle	rectum
20	chr15:75797800-75799400	Strong transcription	Right Ventricle	heart
21	chr15:75797800-75799400	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:75797800-75799400	Strong transcription	Thymus	Thymus
23	chr15:75797800-75799600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
24	chr15:75797800-75799600	Strong transcription	Primary hematopoietic stem cells	blood
25	chr15:75797800-75799600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:75797800-75799600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:75797800-75799600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:75797800-75799600	Strong transcription	Brain Germinal Matrix	brain
29	chr15:75797800-75799600	Strong transcription	Brain Hippocampus Middle	brain
30	chr15:75797800-75799600	Strong transcription	Colonic Mucosa	Colon
31	chr15:75797800-75799600	Strong transcription	Esophagus	oesophagus
32	chr15:75797800-75799600	Strong transcription	Fetal Lung	lung
33	chr15:75797800-75799600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:75797800-75799800	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:75797800-75799800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr15:75797800-75799800	Strong transcription	Spleen	Spleen
37	chr15:75797800-75799800	Strong transcription	HSMMtube	muscle
38	chr15:75797800-75800000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:75797800-75800200	Strong transcription	Lung	lung
40	chr15:75797800-75800400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:75797800-75800800	Strong transcription	Fetal Intestine Large	intestine
42	chr15:75797800-75800800	Strong transcription	Fetal Intestine Small	intestine
43	chr15:75797800-75801000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr15:75797800-75801200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:75797800-75801200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr15:75797800-75801200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:75797800-75801200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:75797800-75801200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:75797800-75801200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:75797800-75801200	Strong transcription	Brain Anterior Caudate	brain

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