Variant report

Variant	rs11085441
Chromosome Location	chr19:21473737-21473738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1055753	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10854043	0.91[EUR][1000 genomes]
rs11085447	0.87[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs1142653	0.91[EUR][1000 genomes]
rs11667770	0.96[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11669588	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11673304	0.80[EUR][1000 genomes]
rs11882553	0.84[EUR][1000 genomes]
rs12459702	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12461384	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12462022	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12610331	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12971736	0.87[EUR][1000 genomes]
rs12972339	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12972580	0.89[EUR][1000 genomes]
rs12972601	0.92[EUR][1000 genomes]
rs12974735	0.90[EUR][1000 genomes]
rs12975081	0.87[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs12975464	0.91[EUR][1000 genomes]
rs12978116	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12980097	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12981564	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs12981735	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs12981775	0.91[EUR][1000 genomes]
rs12981777	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12982162	0.91[EUR][1000 genomes]
rs12982282	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs12982346	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12983426	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12984300	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12984871	0.88[EUR][1000 genomes]
rs17680671	0.86[CEU][hapmap]
rs1781873	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1813234	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1932088	0.92[EUR][1000 genomes]
rs1963531	0.89[EUR][1000 genomes]
rs1963532	0.88[EUR][1000 genomes]
rs2012013	0.81[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs2012038	0.91[EUR][1000 genomes]
rs2061917	0.91[EUR][1000 genomes]
rs2061918	0.90[EUR][1000 genomes]
rs2061919	0.90[EUR][1000 genomes]
rs2086317	0.91[EUR][1000 genomes]
rs2086318	0.90[EUR][1000 genomes]
rs2086320	0.88[EUR][1000 genomes]
rs2088762	0.87[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs2102072	0.87[EUR][1000 genomes]
rs2127404	0.89[EUR][1000 genomes]
rs2127405	0.89[EUR][1000 genomes]
rs2127406	0.89[EUR][1000 genomes]
rs2127407	0.88[EUR][1000 genomes]
rs2127408	0.88[EUR][1000 genomes]
rs2170024	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2170025	0.88[EUR][1000 genomes]
rs2219840	0.91[EUR][1000 genomes]
rs2358982	0.91[EUR][1000 genomes]
rs2358983	0.91[EUR][1000 genomes]
rs2358984	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2358985	0.91[EUR][1000 genomes]
rs2358986	0.89[EUR][1000 genomes]
rs2358988	0.89[EUR][1000 genomes]
rs2358989	0.88[EUR][1000 genomes]
rs2358990	0.89[EUR][1000 genomes]
rs2358991	0.88[EUR][1000 genomes]
rs2358992	0.88[EUR][1000 genomes]
rs2434997	0.88[EUR][1000 genomes]
rs2562456	0.82[JPT][hapmap]
rs2650845	0.83[CHB][hapmap]
rs279797	0.90[YRI][hapmap]
rs279813	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28688205	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2884601	0.91[EUR][1000 genomes]
rs2914638	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2968025	0.83[EUR][1000 genomes]
rs35580411	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4315457	0.87[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs4341872	0.83[CHB][hapmap]
rs4438422	0.91[EUR][1000 genomes]
rs4525621	0.82[EUR][1000 genomes]
rs4566304	0.91[EUR][1000 genomes]
rs4621113	0.96[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap]
rs627522	0.82[JPT][hapmap]
rs6511222	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511229	0.91[EUR][1000 genomes]
rs6511231	0.89[EUR][1000 genomes]
rs6511232	0.89[EUR][1000 genomes]
rs6511233	0.86[EUR][1000 genomes]
rs6511239	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7245920	0.89[EUR][1000 genomes]
rs7247411	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs7248601	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs7249412	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7249636	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7252261	0.87[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs7253178	0.92[EUR][1000 genomes]
rs7254436	0.96[CEU][hapmap]
rs7254762	0.96[CEU][hapmap]
rs7256361	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7257580	0.83[EUR][1000 genomes]
rs7257857	0.96[CEU][hapmap];0.89[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs7258335	0.89[EUR][1000 genomes]
rs7259311	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7260369	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7508030	0.88[EUR][1000 genomes]
rs7508044	0.84[EUR][1000 genomes]
rs7508045	0.83[EUR][1000 genomes]
rs7508072	0.81[EUR][1000 genomes]
rs7508087	0.83[EUR][1000 genomes]
rs7508092	0.88[EUR][1000 genomes]
rs7508104	0.85[EUR][1000 genomes]
rs7508671	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs8099940	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs8103325	0.87[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs8103459	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs8103908	0.89[EUR][1000 genomes]
rs8104017	0.91[EUR][1000 genomes]
rs8107999	0.85[CEU][hapmap]
rs8110690	0.88[EUR][1000 genomes]
rs8110842	0.88[EUR][1000 genomes]
rs8110967	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs8112059	0.92[EUR][1000 genomes]
rs8112583	0.88[EUR][1000 genomes]
rs924487	0.83[CEU][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription 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 target site	41 gene(s)	inside rSNPs	diseases
4	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv578950	chr19:21388995-21477431	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
11	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv2762027	chr19:21465718-21474111	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs11085441	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs11085441	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs11085441	RP11-678G14.2	cis	Thyroid	GTEx
rs11085441	LOC115648	cis	uninvolved skin	skin_eQTL
rs11085441	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs11085441	CTD-2561J22.5	cis	Thyroid	GTEx
rs11085441	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs11085441	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs11085441	LINC00664	cis	Adipose Subcutaneous	GTEx
rs11085441	CTD-2561J22.5	cis	Stomach	GTEx
rs11085441	RP11-678G14.2	cis	Artery Tibial	GTEx
rs11085441	RP11-678G14.2	cis	Nerve Tibial	GTEx
rs11085441	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs11085441	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs11085441	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11085441	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs11085441	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11085441	RP11-678G14.2	cis	Whole Blood	GTEx
rs11085441	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs11085441	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs11085441	RP11-678G14.3	cis	Whole Blood	GTEx
rs11085441	CTD-2561J22.5	cis	lung	GTEx
rs11085441	ZNF429	cis	Muscle Skeletal	GTEx
rs11085441	ZNF429	cis	Whole Blood	GTEx
rs11085441	RP11-678G14.2	cis	lung	GTEx
rs11085441	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11085441	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs11085441	ZNF493	cis	multi-tissue	Pritchard
rs11085441	RP11-420K14.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21465400-21484600	ZNF genes & repeats	Liver	Liver
3	chr19:21467200-21489600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:21468000-21474200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:21469400-21474400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:21470000-21474400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:21470000-21474400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:21470600-21484200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
9	chr19:21471200-21474200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:21471200-21474400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:21471200-21479800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr19:21471600-21474800	Weak transcription	Brain Germinal Matrix	brain
13	chr19:21471600-21479800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:21472000-21476400	Weak transcription	Osteobl	bone
15	chr19:21472000-21481800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:21472200-21474400	Weak transcription	NH-A	brain
17	chr19:21472200-21487600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:21472200-21490400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:21472400-21475200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:21472600-21474200	Weak transcription	HSMMtube	muscle
21	chr19:21472800-21474000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:21472800-21474200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:21472800-21475800	Weak transcription	HSMM	muscle
24	chr19:21473000-21473800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:21473000-21474400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:21473000-21474600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:21473000-21476200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:21473200-21475800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr19:21473200-21476000	Weak transcription	Psoas Muscle	Psoas
30	chr19:21473600-21479400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:21473600-21479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:21473600-21487200	Weak transcription	Right Ventricle	heart

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