Variant report

Variant	rs11732898
Chromosome Location	chr4:6956134-6956135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:6910837..6912550-chr4:6955221..6957525,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10012590	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs10025310	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10516181	0.88[ASN][1000 genomes]
rs10937772	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10937774	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10937776	0.88[ASN][1000 genomes]
rs11938701	0.81[ASN][1000 genomes]
rs11944897	0.81[ASN][1000 genomes]
rs12502513	1.00[CHB][hapmap]
rs12503027	0.81[ASN][1000 genomes]
rs12510715	1.00[CHD][hapmap]
rs12642852	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13107989	0.81[ASN][1000 genomes]
rs13108082	0.81[ASN][1000 genomes]
rs13111887	0.81[ASN][1000 genomes]
rs13122119	1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs13135912	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13148395	0.81[ASN][1000 genomes]
rs13149411	0.87[ASN][1000 genomes]
rs13149923	0.81[ASN][1000 genomes]
rs2301817	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2301818	1.00[CHD][hapmap]
rs2301819	1.00[CHD][hapmap]
rs2359194	0.88[ASN][1000 genomes]
rs3188939	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs34219101	0.94[ASN][1000 genomes]
rs34221933	0.81[ASN][1000 genomes]
rs34335938	0.87[ASN][1000 genomes]
rs34463709	0.87[ASN][1000 genomes]
rs34481892	0.87[ASN][1000 genomes]
rs34959511	0.87[ASN][1000 genomes]
rs35170004	0.87[ASN][1000 genomes]
rs35680216	0.81[ASN][1000 genomes]
rs3857171	0.88[ASN][1000 genomes]
rs3892490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3894945	0.81[ASN][1000 genomes]
rs4234788	0.81[ASN][1000 genomes]
rs4234791	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4234793	0.81[ASN][1000 genomes]
rs4296677	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428285	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4458452	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4544710	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4645214	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689059	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689060	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689560	1.00[CHB][hapmap]
rs4689563	0.87[ASN][1000 genomes]
rs4689564	0.87[ASN][1000 genomes]
rs4689565	0.87[ASN][1000 genomes]
rs4689568	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689573	0.88[ASN][1000 genomes]
rs4689575	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs55822670	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62289166	0.81[ASN][1000 genomes]
rs66530709	0.87[ASN][1000 genomes]
rs66640699	0.87[ASN][1000 genomes]
rs66841627	0.81[ASN][1000 genomes]
rs66931928	0.87[ASN][1000 genomes]
rs66992702	0.87[ASN][1000 genomes]
rs6811496	0.81[ASN][1000 genomes]
rs6816660	0.81[ASN][1000 genomes]
rs6816882	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818744	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6831129	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6834102	0.81[ASN][1000 genomes]
rs6840780	0.81[ASN][1000 genomes]
rs6854776	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs7655563	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7655773	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7658198	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7661462	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7661952	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7673901	0.81[ASN][1000 genomes]
rs7675524	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7685667	0.81[ASN][1000 genomes]
rs7693321	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8180337	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9291126	0.85[CHD][hapmap]

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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3368478	chr4:6954301-6956199	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11732898	GRPEL1	cis	lymphoblastoid	seeQTL
rs11732898	HMX1	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6928000-6969600	Weak transcription	Aorta	Aorta
2	chr4:6945000-6970200	Weak transcription	Hela-S3	cervix
3	chr4:6945800-6965800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:6946600-6969000	Weak transcription	Dnd41	blood
5	chr4:6948600-6962400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr4:6950200-6956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:6950400-6963800	Weak transcription	Small Intestine	intestine
8	chr4:6953600-6960600	Enhancers	Fetal Thymus	thymus
9	chr4:6953800-6960000	Enhancers	Placenta	Placenta
10	chr4:6954000-6957600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr4:6954000-6964000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:6954200-6956800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:6954200-6957800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:6954200-6958000	Weak transcription	Thymus	Thymus
15	chr4:6954200-6958800	Weak transcription	Primary T cells from cord blood	blood
16	chr4:6954400-6956600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:6954400-6957800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr4:6954400-6965800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:6954600-6957000	Weak transcription	Brain Anterior Caudate	brain
20	chr4:6954600-6957800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:6954600-6958000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:6954600-6958200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:6954600-6958200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:6954600-6958400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr4:6954600-6958400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:6954600-6958400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:6954800-6962800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr4:6955000-6962600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:6955200-6956200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr4:6955200-6957800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr4:6955400-6956200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:6955400-6956200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:6955400-6956200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr4:6955400-6956200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:6955400-6956200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:6955400-6956200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:6955400-6956200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr4:6955400-6956200	Enhancers	Fetal Muscle Leg	muscle
39	chr4:6955400-6956200	Flanking Active TSS	Ovary	ovary
40	chr4:6955400-6956200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr4:6955400-6956200	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr4:6955400-6956200	Flanking Active TSS	HMEC	breast
43	chr4:6955400-6956200	Flanking Active TSS	NHEK	skin
44	chr4:6955400-6956400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:6955400-6956600	Enhancers	Gastric	stomach
46	chr4:6955400-6956600	Enhancers	Lung	lung
47	chr4:6955400-6956800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:6955400-6957400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr4:6955400-6957400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr4:6955400-6957600	Enhancers	HUES6 Cell Line	embryonic stem cell

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