Variant report

Variant	rs11054425
Chromosome Location	chr12:11864281-11864282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11802553..11805174-chr12:11862801..11866673,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10845408	0.81[CEU][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs11054421	0.93[JPT][hapmap]
rs11054423	0.87[JPT][hapmap]
rs11054424	0.87[JPT][hapmap]
rs11615175	0.87[MEX][hapmap]
rs12828066	0.87[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17818498	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2187641	0.87[JPT][hapmap]
rs2416882	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2416883	0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs2724588	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2724616	0.87[JPT][hapmap]
rs2724648	0.82[JPT][hapmap]
rs2856321	0.93[JPT][hapmap]
rs2860431	0.87[JPT][hapmap]
rs2900208	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs2954980	0.93[JPT][hapmap]
rs4763720	0.82[CHB][hapmap]
rs972798	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11054425	C12orf36	cis	parietal	SCAN
rs11054425	NECAP1	cis	cerebellum	SCAN
rs11054425	TAS2R42	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11827400-11879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:11838800-11872200	Weak transcription	Primary T cells from cord blood	blood
3	chr12:11841800-11867400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:11844200-11864600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:11848000-11872200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:11848800-11879600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:11849400-11865000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:11853000-11872000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:11853200-11870400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:11854800-11872600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:11855200-11871800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:11855400-11868200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:11857000-11876800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:11857800-11865200	Enhancers	Colon Smooth Muscle	Colon
15	chr12:11858600-11870400	Weak transcription	NHLF	lung
16	chr12:11858800-11864600	Weak transcription	HUVEC	blood vessel
17	chr12:11859200-11872000	Weak transcription	HSMMtube	muscle
18	chr12:11860000-11867600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:11860000-11869800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:11860400-11871600	Weak transcription	Placenta	Placenta
21	chr12:11860600-11865000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:11860600-11868400	Weak transcription	Fetal Intestine Large	intestine
23	chr12:11860600-11869400	Weak transcription	NH-A	brain
24	chr12:11860800-11864600	Enhancers	Stomach Smooth Muscle	stomach
25	chr12:11860800-11865400	Enhancers	Rectal Smooth Muscle	rectum
26	chr12:11860800-11869400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:11860800-11869400	Weak transcription	Esophagus	oesophagus
28	chr12:11860800-11869400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:11860800-11869600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:11860800-11869800	Weak transcription	Colonic Mucosa	Colon
31	chr12:11860800-11869800	Weak transcription	Fetal Kidney	kidney
32	chr12:11860800-11869800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:11860800-11870600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:11860800-11870600	Weak transcription	NHEK	skin
35	chr12:11860800-11871000	Weak transcription	Fetal Brain Male	brain
36	chr12:11860800-11871200	Weak transcription	Lung	lung
37	chr12:11861000-11869800	Weak transcription	HMEC	breast
38	chr12:11861200-11866200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr12:11861200-11866800	Weak transcription	Small Intestine	intestine
40	chr12:11861200-11872400	Strong transcription	Dnd41	blood
41	chr12:11861400-11866800	Weak transcription	Right Atrium	heart
42	chr12:11861400-11869400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:11861400-11869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:11861600-11865200	Weak transcription	Ovary	ovary
45	chr12:11861600-11865400	Weak transcription	Gastric	stomach
46	chr12:11861600-11866800	Weak transcription	Right Ventricle	heart
47	chr12:11861600-11866800	Weak transcription	Thymus	Thymus
48	chr12:11861600-11867600	Weak transcription	Fetal Intestine Small	intestine
49	chr12:11861600-11868400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:11861600-11869800	Weak transcription	Fetal Stomach	stomach

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