Variant report

Variant	rs11047912
Chromosome Location	chr12:25385910-25385911
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	chr12:25382080..25386117-chr12:25388802..25392255,4	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10505959	0.90[JPT][hapmap]
rs10771174	0.81[JPT][hapmap]
rs10771175	1.00[JPT][hapmap]
rs10771176	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10842468	0.88[JPT][hapmap]
rs10842470	1.00[JPT][hapmap]
rs10842490	1.00[JPT][hapmap]
rs10842515	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10842516	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs10842517	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs11047885	1.00[JPT][hapmap]
rs11047914	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11047917	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12227966	1.00[JPT][hapmap]
rs12228638	0.89[JPT][hapmap]
rs12367971	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs17388573	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17388587	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17389103	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs2220196	0.89[JPT][hapmap]
rs3924650	1.00[JPT][hapmap]
rs4313666	1.00[JPT][hapmap]
rs4368021	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs61761150	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7133640	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7134616	1.00[JPT][hapmap]
rs7298444	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7303373	1.00[JPT][hapmap]
rs7309670	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs7311692	0.93[ASN][1000 genomes]
rs7315339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7960917	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7968023	0.97[ASN][1000 genomes]
rs7971062	0.89[JPT][hapmap]
rs7971288	0.89[JPT][hapmap]
rs7973450	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7976254	0.90[JPT][hapmap]
rs7976355	1.00[JPT][hapmap]
rs7980769	0.88[GIH][hapmap];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	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv898923	chr12:25357680-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv898924	chr12:25357680-25398972	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv557798	chr12:25359841-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv898925	chr12:25367669-25398972	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv898926	chr12:25367669-25408047	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv470279	chr12:25384658-25399121	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11047912	BCAT1	cis	lymphoblastoid	seeQTL
rs11047912	GOLT1B	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
3	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
4	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
5	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:25349400-25388600	Weak transcription	NHLF	lung
7	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
10	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
11	chr12:25349600-25389000	Weak transcription	Brain Angular Gyrus	brain
12	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:25349800-25386200	Weak transcription	Hela-S3	cervix
18	chr12:25349800-25390200	Weak transcription	K562	blood
19	chr12:25350000-25402800	Weak transcription	Ovary	ovary
20	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:25354400-25402200	Weak transcription	Pancreas	Pancrea
22	chr12:25354600-25389000	Weak transcription	HSMMtube	muscle
23	chr12:25355800-25396000	Weak transcription	Small Intestine	intestine
24	chr12:25356600-25402600	Weak transcription	Fetal Heart	heart
25	chr12:25360800-25388600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:25360800-25389200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:25360800-25402200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:25361000-25388000	Weak transcription	A549	lung
29	chr12:25361000-25388600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:25361000-25388800	Weak transcription	Esophagus	oesophagus
31	chr12:25361000-25395800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:25361000-25402600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:25361000-25402600	Weak transcription	Fetal Brain Female	brain
34	chr12:25361200-25388400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:25361200-25389200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:25362000-25402400	Weak transcription	HepG2	liver
37	chr12:25363400-25388000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:25365200-25393800	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:25367800-25388200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:25369600-25388200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:25372400-25402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:25373000-25393800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:25373400-25388200	Weak transcription	GM12878-XiMat	blood
44	chr12:25374400-25391600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:25374600-25388400	Weak transcription	Thymus	Thymus
46	chr12:25374600-25388600	Weak transcription	Lung	lung
47	chr12:25374800-25402600	Weak transcription	Placenta	Placenta
48	chr12:25375000-25388600	Weak transcription	Fetal Stomach	stomach
49	chr12:25375000-25402800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:25376800-25388600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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