Variant report

Variant	rs2669568
Chromosome Location	chr12:26197687-26197688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10505989	0.90[JPT][hapmap]
rs10771254	0.82[CHB][hapmap]
rs11494759	0.82[CHB][hapmap]
rs12426668	0.92[JPT][hapmap]
rs1355707	0.82[CHB][hapmap]
rs1495649	0.81[JPT][hapmap]
rs16929780	0.83[JPT][hapmap]
rs16929815	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs16929860	0.96[CHD][hapmap];0.83[JPT][hapmap]
rs16929894	0.83[JPT][hapmap]
rs16929895	0.83[JPT][hapmap]
rs16929904	0.82[JPT][hapmap]
rs16929970	0.92[JPT][hapmap]
rs16929998	0.92[JPT][hapmap]
rs1797943	0.82[CHB][hapmap]
rs2137550	0.92[JPT][hapmap]
rs2343200	0.83[JPT][hapmap]
rs2643943	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2669560	0.82[CHB][hapmap]
rs2669565	0.92[JPT][hapmap]
rs2669566	0.92[JPT][hapmap]
rs2729626	0.92[JPT][hapmap]
rs2729633	0.82[CHB][hapmap]
rs2729638	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729643	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]
rs2729644	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2729649	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[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];0.80[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]
rs924052	0.80[CHB][hapmap]
rs949849	0.87[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2669568	KLHDC5	cis	parietal	SCAN
rs2669568	GBX2	trans	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26186000-26200400	Weak transcription	Right Ventricle	heart
2	chr12:26187200-26200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:26192400-26228600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:26193600-26200600	Weak transcription	Left Ventricle	heart
5	chr12:26194600-26199000	Enhancers	NHDF-Ad	bronchial
6	chr12:26194800-26198600	Enhancers	NH-A	brain
7	chr12:26194800-26199000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:26195200-26197800	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr12:26195200-26201200	Enhancers	Colon Smooth Muscle	Colon
10	chr12:26195600-26198400	Weak transcription	HSMM	muscle
11	chr12:26195600-26198600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:26195600-26200600	Weak transcription	HUVEC	blood vessel
13	chr12:26196000-26197800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:26196000-26199000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:26196200-26208200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:26196400-26199800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:26196400-26200400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:26196400-26200400	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:26196400-26200600	Weak transcription	Fetal Heart	heart
20	chr12:26196400-26201000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:26196400-26219800	Weak transcription	Fetal Kidney	kidney
22	chr12:26196600-26200400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:26196600-26200400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:26196600-26200400	Weak transcription	Lung	lung
25	chr12:26196600-26200600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:26196800-26197800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:26196800-26199800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:26196800-26200400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:26196800-26200400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:26196800-26200800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:26196800-26201400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:26197000-26198400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:26197000-26198600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:26197000-26198800	Enhancers	Osteobl	bone
35	chr12:26197000-26200000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:26197000-26200400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:26197000-26201600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:26197000-26208200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:26197200-26197800	Enhancers	Brain Angular Gyrus	brain
40	chr12:26197200-26198000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:26197200-26198200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr12:26197200-26198800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:26197200-26199200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:26197200-26199200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:26197200-26199800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:26197200-26200000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:26197200-26200000	Enhancers	Brain Anterior Caudate	brain
48	chr12:26197200-26200000	Enhancers	Brain Hippocampus Middle	brain
49	chr12:26197200-26200400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:26197200-26200400	Weak transcription	Ovary	ovary

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