Variant report

Variant	rs135642
Chromosome Location	chr22:28538999-28539000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10483141	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10483148	1.00[CHB][hapmap]
rs12170637	1.00[CHB][hapmap]
rs1297607	1.00[CHB][hapmap]
rs13055409	0.89[AFR][1000 genomes]
rs13057007	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs13057948	0.82[CEU][hapmap]
rs13058493	0.90[GIH][hapmap];1.00[MEX][hapmap]
rs134488	1.00[CHB][hapmap]
rs135113	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs135637	1.00[ASN][1000 genomes]
rs135641	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs135643	1.00[ASN][1000 genomes]
rs135644	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs135645	1.00[CHB][hapmap]
rs135649	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs135655	1.00[ASN][1000 genomes]
rs135659	1.00[ASN][1000 genomes]
rs138646	1.00[CHB][hapmap]
rs138680	1.00[CHB][hapmap]
rs1569700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16985862	1.00[ASN][1000 genomes]
rs16985870	1.00[ASN][1000 genomes]
rs16985925	1.00[ASN][1000 genomes]
rs16985933	1.00[ASN][1000 genomes]
rs16986177	1.00[CHB][hapmap]
rs16986254	1.00[CHB][hapmap]
rs16986257	1.00[CHB][hapmap]
rs16986266	1.00[CHB][hapmap]
rs2038286	1.00[ASN][1000 genomes]
rs2038287	1.00[CHB][hapmap]
rs2143420	1.00[CHB][hapmap]
rs2345011	1.00[CHB][hapmap]
rs28360522	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs35286067	0.82[AFR][1000 genomes]
rs470101	1.00[CHB][hapmap]
rs7285440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs731050	1.00[ASN][1000 genomes]
rs767919	0.82[CEU][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs135642	SIX3	trans	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28533600-28542800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:28533800-28559000	Weak transcription	Aorta	Aorta
3	chr22:28534200-28545200	Enhancers	Fetal Lung	lung
4	chr22:28534400-28544000	Enhancers	Fetal Brain Male	brain
5	chr22:28534600-28541000	Enhancers	Fetal Stomach	stomach
6	chr22:28535400-28539400	Enhancers	HMEC	breast
7	chr22:28535400-28541200	Enhancers	Colon Smooth Muscle	Colon
8	chr22:28535600-28539200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr22:28535600-28540400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr22:28535800-28539000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr22:28535800-28539000	Enhancers	NHEK	skin
12	chr22:28535800-28540200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr22:28535800-28540400	Enhancers	Fetal Heart	heart
14	chr22:28535800-28540800	Enhancers	Rectal Smooth Muscle	rectum
15	chr22:28536000-28542200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr22:28536000-28544400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr22:28536200-28542400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr22:28536200-28546600	Weak transcription	Left Ventricle	heart
19	chr22:28536200-28549600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr22:28536400-28539000	Weak transcription	Right Atrium	heart
21	chr22:28536400-28542200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr22:28536800-28543800	Enhancers	Fetal Brain Female	brain
23	chr22:28537000-28539800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:28537200-28541000	Enhancers	Fetal Kidney	kidney
25	chr22:28537200-28558800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr22:28537400-28539000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr22:28537400-28539400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr22:28537400-28542400	Weak transcription	Right Ventricle	heart
29	chr22:28537600-28539400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr22:28538000-28539200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr22:28538000-28539400	Enhancers	Ovary	ovary
32	chr22:28538000-28539400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr22:28538000-28542200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr22:28538200-28539200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr22:28538200-28539400	Enhancers	Brain Cingulate Gyrus	brain
36	chr22:28538200-28539800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr22:28538200-28540200	Enhancers	Brain Anterior Caudate	brain
38	chr22:28538400-28539000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr22:28538400-28539200	Enhancers	Brain Germinal Matrix	brain
40	chr22:28538400-28539200	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr22:28538400-28539800	Enhancers	Brain Hippocampus Middle	brain
42	chr22:28538400-28540200	Enhancers	HSMM	muscle
43	chr22:28538400-28540600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr22:28538400-28540800	Weak transcription	Lung	lung
45	chr22:28538400-28540800	Enhancers	NHLF	lung
46	chr22:28538400-28543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr22:28538400-28544800	Weak transcription	Dnd41	blood
48	chr22:28538600-28539000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr22:28538600-28539000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr22:28538600-28539000	Enhancers	Rectal Mucosa Donor 29	rectum

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