Variant report

Variant	rs876701
Chromosome Location	chr11:46370767-46370768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:46257250..46262210-chr11:46367431..46371476,7	K562	blood:
2	chr11:46370608..46372657-chr11:46396272..46398453,2	K562	blood:
3	chr11:46369907..46371669-chr11:46372067..46373780,2	MCF-7	breast:
4	chr11:46368689..46375486-chr11:46400770..46406098,12	K562	blood:
5	chr11:46369976..46372560-chr11:46412510..46415040,2	K562	blood:
6	chr11:46368921..46370887-chr11:46401609..46403776,2	MCF-7	breast:
7	chr11:46257890..46267047-chr11:46362753..46375455,17	K562	blood:
8	chr11:46362000..46364910-chr11:46370299..46373076,2	K562	blood:
9	chr11:46366347..46371334-chr11:46384499..46389085,13	MCF-7	breast:
10	chr11:46197522..46200380-chr11:46369487..46372078,2	K562	blood:
11	chr11:46370537..46375565-chr11:46394528..46400368,5	MCF-7	breast:
12	chr11:46143580..46145236-chr11:46369479..46372129,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254639	Chromatin interaction
ENSG00000110492	Chromatin interaction
ENSG00000149091	Chromatin interaction
ENSG00000264102	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10160701	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10838602	0.89[EUR][1000 genomes]
rs11038897	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11038900	0.89[EUR][1000 genomes]
rs11038906	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs11038914	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs11038919	0.88[EUR][1000 genomes]
rs11038927	0.87[EUR][1000 genomes]
rs11819869	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12272795	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs12283172	0.81[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12292425	0.85[EUR][1000 genomes]
rs12295266	0.86[EUR][1000 genomes]
rs12573978	0.91[EUR][1000 genomes]
rs12574250	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs12574668	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12575519	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12576115	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12576317	0.91[EUR][1000 genomes]
rs12576359	0.89[EUR][1000 genomes]
rs12577142	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12578042	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs1472001	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1489192	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs16938506	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]
rs17197116	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2046768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2067482	0.91[EUR][1000 genomes]
rs2171667	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs2171668	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2279465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291487	1.00[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2864072	0.91[EUR][1000 genomes]
rs2864076	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2902858	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs34406563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35324223	0.83[EUR][1000 genomes]
rs35623865	0.84[EUR][1000 genomes]
rs3740974	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3740977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3802888	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs3809047	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs55657382	0.84[EUR][1000 genomes]
rs55661562	0.84[EUR][1000 genomes]
rs57535407	0.91[EUR][1000 genomes]
rs58147945	0.89[EUR][1000 genomes]
rs59319338	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60722866	0.82[EUR][1000 genomes]
rs61882678	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61882682	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61882683	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61882691	0.89[EUR][1000 genomes]
rs61882701	0.91[EUR][1000 genomes]
rs61882702	0.91[EUR][1000 genomes]
rs61882706	0.90[EUR][1000 genomes]
rs61882709	0.91[EUR][1000 genomes]
rs61882710	0.91[EUR][1000 genomes]
rs61882711	0.91[EUR][1000 genomes]
rs61882712	0.89[EUR][1000 genomes]
rs61882720	0.88[EUR][1000 genomes]
rs61882743	0.87[EUR][1000 genomes]
rs61882746	0.90[EUR][1000 genomes]
rs61882748	0.91[EUR][1000 genomes]
rs61882750	0.90[EUR][1000 genomes]
rs61882756	0.84[EUR][1000 genomes]
rs61882757	0.86[EUR][1000 genomes]
rs61882758	0.86[EUR][1000 genomes]
rs61884264	0.84[EUR][1000 genomes]
rs6485682	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs6485685	0.84[EUR][1000 genomes]
rs7108770	0.83[EUR][1000 genomes]
rs7112229	0.81[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7122039	0.85[EUR][1000 genomes]
rs7125907	0.85[EUR][1000 genomes]
rs7127529	0.90[EUR][1000 genomes]
rs7130141	0.87[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs73449983	0.86[EUR][1000 genomes]
rs7481312	0.88[EUR][1000 genomes]
rs7484002	0.84[EUR][1000 genomes]
rs7924401	0.85[EUR][1000 genomes]
rs7930103	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs7932866	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap]
rs7936413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7946705	0.91[EUR][1000 genomes]
rs7951579	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7951870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv554201	chr11:46281835-46422686	Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv825867	chr11:46303184-46425613	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS 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	21 gene(s)	inside rSNPs	diseases
3	esv1797501	chr11:46315437-46402521	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	esv1811345	chr11:46317062-46438072	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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	22 gene(s)	inside rSNPs	diseases
5	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
6	nsv897316	chr11:46349631-46417815	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
7	nsv897317	chr11:46363411-46417815	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs876701	C11orf49	cis	parietal	SCAN
rs876701	ATG13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46367800-46370800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:46368600-46370800	Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr11:46369400-46370800	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr11:46369400-46370800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:46369400-46370800	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr11:46369400-46370800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr11:46369400-46371000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr11:46369400-46371000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr11:46369400-46371000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr11:46369400-46371800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:46369400-46372400	Enhancers	Fetal Brain Male	brain
12	chr11:46369600-46370800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:46369600-46370800	Flanking Active TSS	Fetal Thymus	thymus
14	chr11:46369600-46370800	Flanking Active TSS	Lung	lung
15	chr11:46369600-46370800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr11:46369600-46370800	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr11:46369600-46370800	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr11:46369600-46371000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:46369600-46371000	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr11:46369600-46371000	Flanking Active TSS	Hela-S3	cervix
21	chr11:46369600-46371200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:46369600-46371400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:46369600-46371400	Flanking Active TSS	Dnd41	blood
24	chr11:46369600-46371600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr11:46369600-46372200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr11:46369600-46372800	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr11:46369800-46370800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr11:46369800-46370800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr11:46369800-46370800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:46369800-46370800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:46369800-46370800	Flanking Active TSS	Fetal Heart	heart
32	chr11:46369800-46370800	Flanking Active TSS	HMEC	breast
33	chr11:46369800-46371000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:46369800-46371400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:46369800-46371400	Flanking Active TSS	GM12878-XiMat	blood
36	chr11:46369800-46371600	Flanking Active TSS	Thymus	Thymus
37	chr11:46369800-46371800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr11:46369800-46372800	Weak transcription	Ovary	ovary
39	chr11:46370000-46370800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:46370000-46370800	Flanking Active TSS	HepG2	liver
41	chr11:46370000-46370800	Flanking Active TSS	HSMM	muscle
42	chr11:46370000-46371200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:46370000-46371400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr11:46370000-46384000	Weak transcription	Fetal Kidney	kidney
45	chr11:46370000-46395800	Weak transcription	Aorta	Aorta
46	chr11:46370200-46370800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:46370200-46370800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:46370200-46370800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr11:46370200-46370800	Enhancers	Fetal Lung	lung
50	chr11:46370200-46370800	Active TSS	Rectal Smooth Muscle	rectum

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