Variant report

Variant	rs2729643
Chromosome Location	chr12:26201469-26201470
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:26200605..26203290-chr12:26207731..26209424,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10505989	0.90[JPT][hapmap]
rs12426668	0.92[JPT][hapmap]
rs1495649	0.81[JPT][hapmap]
rs16929780	0.83[JPT][hapmap]
rs16929815	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap]
rs16929860	0.86[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap]
rs16929894	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs16929895	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs16929904	0.82[JPT][hapmap]
rs16929970	0.92[JPT][hapmap]
rs16929998	0.92[JPT][hapmap]
rs2137550	0.92[JPT][hapmap]
rs2343200	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2643943	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2669565	0.92[JPT][hapmap]
rs2669566	0.92[JPT][hapmap]
rs2669568	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[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];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729626	0.92[JPT][hapmap]
rs2729638	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2729649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840134	0.88[EUR][1000 genomes]
rs4963644	0.83[JPT][hapmap]
rs4963947	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs4963952	0.92[JPT][hapmap]
rs6487526	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73079069	0.85[ASN][1000 genomes]
rs7961722	0.92[JPT][hapmap]
rs885208	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs949849	0.81[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2729643	GBX2	trans	parietal	SCAN
rs2729643	KLHDC5	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26192400-26228600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:26196200-26208200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:26196400-26219800	Weak transcription	Fetal Kidney	kidney
4	chr12:26197000-26201600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:26197000-26208200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:26197200-26206000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:26197200-26209400	Weak transcription	NHLF	lung
8	chr12:26197200-26211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:26197200-26228600	Weak transcription	Aorta	Aorta
10	chr12:26197600-26209200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:26197800-26209000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:26199200-26220200	Weak transcription	Brain Substantia Nigra	brain
13	chr12:26199400-26221600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:26199800-26201600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr12:26200000-26205400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:26200000-26205800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:26200400-26201600	Enhancers	Psoas Muscle	Psoas
18	chr12:26200400-26201600	Enhancers	Right Atrium	heart
19	chr12:26200600-26201600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr12:26200600-26201600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr12:26200600-26209200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:26200800-26201600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:26200800-26202000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:26200800-26206400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:26200800-26207400	Weak transcription	Pancreas	Pancrea
26	chr12:26200800-26208800	Weak transcription	Lung	lung
27	chr12:26200800-26209200	Weak transcription	Fetal Brain Male	brain
28	chr12:26200800-26229000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:26201000-26201600	Enhancers	Right Ventricle	heart
30	chr12:26201000-26204800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:26201000-26205400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:26201000-26205400	Weak transcription	HUVEC	blood vessel
33	chr12:26201000-26205400	Weak transcription	NH-A	brain
34	chr12:26201000-26206400	Weak transcription	Ovary	ovary
35	chr12:26201000-26206600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:26201000-26207400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:26201000-26220800	Weak transcription	Left Ventricle	heart
38	chr12:26201000-26223400	Weak transcription	Fetal Muscle Leg	muscle
39	chr12:26201200-26205400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:26201200-26205400	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:26201200-26206600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:26201200-26206600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:26201200-26210800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:26201200-26234600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:26201400-26201600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:26201400-26201600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr12:26201400-26204800	Weak transcription	NHDF-Ad	bronchial
48	chr12:26201400-26205400	Weak transcription	Osteobl	bone
49	chr12:26201400-26206400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:26201400-26206400	Weak transcription	Fetal Heart	heart

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