Variant report

Variant	rs11052241
Chromosome Location	chr12:9811948-9811949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:9799797..9802431-chr12:9811559..9813864,2	MCF-7	breast:
2	chr12:9811398..9813621-chr12:9843826..9845661,2	MCF-7	breast:
3	chr12:9807912..9810115-chr12:9811259..9815129,3	MCF-7	breast:
4	chr12:9810242..9813132-chr12:9813704..9817912,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069493	Chromatin interaction
ENSG00000256442	Chromatin interaction
ENSG00000256594	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10047657	0.81[AFR][1000 genomes]
rs1008611	1.00[JPT][hapmap]
rs10466762	1.00[JPT][hapmap]
rs10743820	1.00[JPT][hapmap]
rs10743822	1.00[JPT][hapmap]
rs10771996	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10772005	1.00[JPT][hapmap]
rs10772006	1.00[JPT][hapmap]
rs10772104	1.00[JPT][hapmap]
rs10772119	1.00[JPT][hapmap]
rs10772120	1.00[JPT][hapmap]
rs10844325	0.81[AFR][1000 genomes]
rs10844350	1.00[JPT][hapmap]
rs10844351	1.00[JPT][hapmap]
rs10844359	1.00[JPT][hapmap]
rs10844372	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844418	1.00[JPT][hapmap]
rs10844424	1.00[JPT][hapmap]
rs10844429	1.00[JPT][hapmap]
rs10844780	1.00[JPT][hapmap]
rs11052234	1.00[JPT][hapmap]
rs11052254	1.00[JPT][hapmap]
rs11052430	1.00[JPT][hapmap]
rs11053051	1.00[JPT][hapmap]
rs1108452	1.00[CHB][hapmap]
rs12366653	1.00[JPT][hapmap]
rs12368445	1.00[JPT][hapmap]
rs12578928	1.00[JPT][hapmap]
rs12810851	1.00[JPT][hapmap]
rs12823699	1.00[JPT][hapmap]
rs12824491	1.00[JPT][hapmap]
rs12825507	1.00[JPT][hapmap]
rs12828602	1.00[JPT][hapmap]
rs12830419	1.00[JPT][hapmap]
rs12831453	1.00[JPT][hapmap]
rs1560008	1.00[JPT][hapmap]
rs16913477	1.00[JPT][hapmap]
rs1863871	1.00[JPT][hapmap]
rs1863875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990533	1.00[JPT][hapmap]
rs2114869	1.00[JPT][hapmap]
rs2114872	1.00[JPT][hapmap]
rs2401396	1.00[JPT][hapmap]
rs2401397	1.00[JPT][hapmap]
rs2401398	1.00[JPT][hapmap]
rs3176800	1.00[JPT][hapmap]
rs3176802	1.00[JPT][hapmap]
rs3176806	1.00[JPT][hapmap]
rs6416258	1.00[JPT][hapmap]
rs6488065	1.00[JPT][hapmap]
rs6488100	1.00[CHB][hapmap]
rs704223	1.00[JPT][hapmap]
rs7132037	1.00[JPT][hapmap]
rs7302110	1.00[JPT][hapmap]
rs7302746	1.00[JPT][hapmap]
rs7304321	1.00[JPT][hapmap]
rs7304464	1.00[JPT][hapmap]
rs7309800	1.00[JPT][hapmap]
rs7310568	1.00[JPT][hapmap]
rs7310790	1.00[JPT][hapmap]
rs7310897	1.00[JPT][hapmap]
rs7311421	1.00[JPT][hapmap]
rs7311574	1.00[JPT][hapmap]
rs7311945	1.00[JPT][hapmap]
rs7312624	1.00[JPT][hapmap]
rs7961416	1.00[JPT][hapmap]
rs7962321	1.00[JPT][hapmap]
rs7974871	1.00[JPT][hapmap]
rs7978187	1.00[JPT][hapmap]
rs929615	1.00[JPT][hapmap]
rs9630265	1.00[JPT][hapmap]
rs982511	1.00[JPT][hapmap]
rs9919786	1.00[JPT][hapmap]

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	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11052241	KLRC3	cis	parietal	SCAN
rs11052241	VAMP1	cis	cerebellum	SCAN
rs11052241	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11052241	KLRC4	cis	parietal	SCAN
rs11052241	CLEC2D	cis	Adipose Subcutaneous	GTEx
rs11052241	GNB3	cis	cerebellum	SCAN
rs11052241	RP11-75L1.2	cis	Adipose Subcutaneous	GTEx
rs11052241	KLRK1	cis	parietal	SCAN
rs11052241	GPR162	cis	parietal	SCAN
rs11052241	CLEC2D	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
4	chr12:9802600-9812800	Weak transcription	Ovary	ovary
5	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:9803000-9812200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
8	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
10	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
12	chr12:9803200-9812400	Weak transcription	Liver	Liver
13	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:9803600-9812200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
16	chr12:9804000-9814200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:9804200-9812400	Weak transcription	Brain Anterior Caudate	brain
18	chr12:9804200-9813200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:9804200-9814200	Weak transcription	Colonic Mucosa	Colon
20	chr12:9804200-9814600	Weak transcription	Lung	lung
21	chr12:9804200-9815000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:9804400-9812200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:9804400-9812200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:9804400-9812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:9804400-9814600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:9804400-9820400	Weak transcription	HUVEC	blood vessel
27	chr12:9804600-9820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:9804600-9820000	Weak transcription	HMEC	breast
29	chr12:9804600-9820200	Weak transcription	NHEK	skin
30	chr12:9805000-9813800	Weak transcription	K562	blood
31	chr12:9805600-9813600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
32	chr12:9805600-9815000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:9805600-9819400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:9805800-9818200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:9806000-9813400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:9806000-9813400	Weak transcription	Fetal Brain Male	brain
37	chr12:9806000-9814400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:9806000-9814800	Strong transcription	Fetal Thymus	thymus
39	chr12:9806000-9815400	Strong transcription	Fetal Intestine Large	intestine
40	chr12:9806000-9818000	Strong transcription	Fetal Muscle Leg	muscle
41	chr12:9806200-9814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:9806200-9815800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:9806200-9818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:9806200-9818200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:9806200-9819000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:9806200-9821600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:9806400-9813000	Strong transcription	HepG2	liver
48	chr12:9806400-9813200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:9806400-9814400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:9806400-9815200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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