Variant report

Variant	rs16938506
Chromosome Location	chr11:46454313-46454314
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:46452244..46454737-chr11:46456753..46459294,3	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10160701	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838602	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038897	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038900	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11038906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038914	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11038927	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11819869	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12272795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12283172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12292425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12295266	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12573978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12575519	0.98[EUR][1000 genomes]
rs12576115	0.94[EUR][1000 genomes]
rs12576317	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12576359	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12577142	0.95[EUR][1000 genomes]
rs12578042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472001	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17197116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2046768	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2067482	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2171667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279465	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2291487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864072	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34406563	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs35324223	0.86[EUR][1000 genomes]
rs35623865	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs3740974	0.98[EUR][1000 genomes]
rs3740977	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3802888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809047	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs4307676	0.87[EUR][1000 genomes]
rs55657382	0.91[EUR][1000 genomes]
rs55661562	0.91[EUR][1000 genomes]
rs55750336	0.90[ASN][1000 genomes]
rs55896955	0.80[EUR][1000 genomes]
rs57535407	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58147945	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59319338	0.95[EUR][1000 genomes]
rs60722866	0.88[EUR][1000 genomes]
rs60932698	0.89[EUR][1000 genomes]
rs61882674	0.82[EUR][1000 genomes]
rs61882678	0.90[EUR][1000 genomes]
rs61882682	0.96[EUR][1000 genomes]
rs61882683	0.92[EUR][1000 genomes]
rs61882691	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882701	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882702	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61882706	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61882709	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882710	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882711	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882712	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882720	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882743	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882746	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882748	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882750	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882756	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882757	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882758	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884262	0.85[EUR][1000 genomes]
rs61884264	0.93[EUR][1000 genomes]
rs61884271	0.89[EUR][1000 genomes]
rs61884273	0.87[EUR][1000 genomes]
rs61884274	0.87[EUR][1000 genomes]
rs61884292	0.80[EUR][1000 genomes]
rs6485682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6485685	0.91[EUR][1000 genomes]
rs7108770	0.91[EUR][1000 genomes]
rs7109698	0.81[EUR][1000 genomes]
rs7112229	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7122039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7125907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7126316	0.86[EUR][1000 genomes]
rs7126343	0.87[EUR][1000 genomes]
rs7127529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7128092	0.86[EUR][1000 genomes]
rs7130141	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73449983	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7481312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7484002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs756343	0.90[ASN][1000 genomes]
rs7924401	0.92[EUR][1000 genomes]
rs7930103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs7936413	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7946705	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7951579	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951870	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs876701	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]

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	nsv554202	chr11:46334239-46469900	Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1050614	chr11:46414720-46496732	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541029	chr11:46442658-46460232	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16938506	C11orf49	cis	parietal	SCAN
rs16938506	ATG13	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46417800-46463400	Weak transcription	Fetal Brain Male	brain
2	chr11:46426800-46468800	Weak transcription	Psoas Muscle	Psoas
3	chr11:46430200-46456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:46430600-46455000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:46433600-46466400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:46436400-46454400	Weak transcription	A549	lung
7	chr11:46436600-46466400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:46437400-46455000	Weak transcription	Stomach Mucosa	stomach
9	chr11:46438000-46461400	Strong transcription	Primary T cells from cord blood	blood
10	chr11:46438400-46454400	Weak transcription	Brain Angular Gyrus	brain
11	chr11:46438400-46457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:46438400-46459600	Strong transcription	Dnd41	blood
13	chr11:46440400-46466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:46443200-46454800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:46443400-46454400	Weak transcription	Brain Germinal Matrix	brain
16	chr11:46443800-46454800	Weak transcription	NHLF	lung
17	chr11:46444000-46456600	Weak transcription	Fetal Heart	heart
18	chr11:46444600-46454600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:46444800-46457200	Weak transcription	Small Intestine	intestine
20	chr11:46445800-46456600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr11:46445800-46458000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:46447000-46457400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:46447200-46457600	Strong transcription	Fetal Stomach	stomach
24	chr11:46447600-46457600	Strong transcription	Liver	Liver
25	chr11:46447600-46457600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:46447800-46456200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:46447800-46460600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr11:46448200-46457800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr11:46448600-46457600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:46448800-46457600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:46448800-46457600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr11:46449000-46456600	Strong transcription	Fetal Muscle Leg	muscle
33	chr11:46449000-46457400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr11:46449600-46457800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr11:46450000-46454400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:46450000-46457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr11:46450400-46458000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr11:46450600-46456800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:46450800-46456600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:46450800-46456800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:46450800-46457600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:46451000-46454400	Weak transcription	Hela-S3	cervix
43	chr11:46451000-46454800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:46451000-46456600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr11:46451000-46456800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr11:46451000-46457000	Strong transcription	Fetal Intestine Large	intestine
47	chr11:46451000-46457400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:46451000-46457400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr11:46451000-46457400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:46451000-46457400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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