Variant report

Variant	rs2305982
Chromosome Location	chr11:47857168-47857169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47857004..47860326-chr11:47862675..47865645,4	MCF-7	breast:
2	chr11:47847046..47849483-chr11:47857033..47859770,3	MCF-7	breast:
3	chr11:47855476..47858340-chr11:47867980..47871002,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271557	Chromatin interaction
ENSG00000030066	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11039387	0.98[ASN][1000 genomes]
rs11819979	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11820480	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474056	0.80[ASN][1000 genomes]
rs16938631	1.00[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs17198607	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs17791016	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1872167	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2138767	0.81[ASN][1000 genomes]
rs2305983	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2869531	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869532	0.88[ASN][1000 genomes]
rs4303192	0.82[EUR][1000 genomes]
rs4752786	0.81[ASN][1000 genomes]
rs4752791	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752872	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752877	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752879	0.93[ASN][1000 genomes]
rs57436966	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58357937	0.88[ASN][1000 genomes]
rs59205786	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59652089	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60515486	0.85[ASN][1000 genomes]
rs6485772	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485774	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6485783	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];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6485784	1.00[ASN][1000 genomes]
rs6485788	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs6485789	0.92[AFR][1000 genomes]
rs7120737	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7121264	0.88[ASN][1000 genomes]
rs7124949	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924699	0.94[ASN][1000 genomes]
rs7927611	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931089	0.80[ASN][1000 genomes]
rs7939069	1.00[ASW][hapmap];0.85[LWK][hapmap];0.94[MKK][hapmap]
rs7942031	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7945911	0.83[ASN][1000 genomes]
rs7946766	1.00[CEU][hapmap];0.94[TSI][hapmap]
rs7952204	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
4	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2305982	ATG13	cis	parietal	SCAN
rs2305982	SLC35C1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47795400-47866600	Strong transcription	Fetal Thymus	thymus
3	chr11:47795400-47868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47796200-47867400	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr11:47796200-47868200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:47796200-47868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:47796200-47868400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:47796200-47868400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:47796200-47868600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:47796400-47858800	Strong transcription	Liver	Liver
11	chr11:47796400-47867600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:47796600-47868600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr11:47798000-47868000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:47798400-47864800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:47807000-47865600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr11:47820000-47864800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr11:47831800-47868000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:47837200-47857200	Weak transcription	Small Intestine	intestine
19	chr11:47840600-47863600	Weak transcription	Stomach Mucosa	stomach
20	chr11:47846600-47864200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:47846600-47867000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:47847000-47868200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:47847200-47867400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr11:47847600-47868000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:47847600-47868800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr11:47847800-47865600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:47848200-47867200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:47848800-47861800	Strong transcription	Ovary	ovary
29	chr11:47849200-47862600	Strong transcription	Brain Germinal Matrix	brain
30	chr11:47849800-47865800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr11:47850000-47867600	Strong transcription	Primary B cells from cord blood	blood
32	chr11:47850000-47868400	Strong transcription	Fetal Lung	lung
33	chr11:47850200-47864000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr11:47850200-47867400	Strong transcription	Primary T cells from cord blood	blood
35	chr11:47850600-47868400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:47851200-47865200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:47851400-47868600	Strong transcription	Placenta	Placenta
38	chr11:47851600-47860000	Strong transcription	Fetal Brain Male	brain
39	chr11:47851600-47865800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:47851600-47866200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr11:47851600-47867400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:47851800-47863600	Strong transcription	Dnd41	blood
43	chr11:47851800-47864600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr11:47851800-47864800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr11:47851800-47865200	Strong transcription	Adipose Nuclei	Adipose
46	chr11:47851800-47865400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:47851800-47867600	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr11:47851800-47868000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:47851800-47868000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:47852000-47863000	Strong transcription	Hela-S3	cervix

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