Variant report

Variant	rs12550310
Chromosome Location	chr8:124114589-124114590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10101590	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10505431	0.83[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10956116	0.97[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs11774489	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs11774656	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11781484	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11785137	0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11786727	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs12541269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12541786	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12543807	0.84[JPT][hapmap]
rs13439161	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs16897969	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs2385163	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2385164	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2891695	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4870845	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs4870846	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4870847	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4871345	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs4871346	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4871347	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7012815	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7836014	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs952655	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs952656	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][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	nsv1032827	chr8:123668081-124270400	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv529364	chr8:123763846-124373809	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv429939	chr8:124027819-124180819	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1028933	chr8:124065484-124181718	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv1015490	chr8:124103255-124150990	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1015249	chr8:124103504-124373949	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv539741	chr8:124103504-124373949	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12550310	WDR67	cis	parietal	SCAN
rs12550310	ANXA13	cis	parietal	SCAN
rs12550310	KLHL38	cis	cerebellum	SCAN
rs12550310	WDR67	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:124085800-124118800	Weak transcription	Small Intestine	intestine
2	chr8:124086000-124115600	Weak transcription	Right Ventricle	heart
3	chr8:124086000-124115800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:124086000-124116200	Weak transcription	Brain Substantia Nigra	brain
5	chr8:124086000-124116600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr8:124086000-124117200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr8:124086000-124117200	Weak transcription	HSMMtube	muscle
8	chr8:124086000-124146400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr8:124086000-124154600	Weak transcription	Aorta	Aorta
10	chr8:124086000-124158400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:124086000-124168800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr8:124086000-124169000	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:124086200-124115800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr8:124086200-124122000	Weak transcription	Spleen	Spleen
15	chr8:124086200-124142200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr8:124086200-124146400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr8:124086200-124168800	Weak transcription	Esophagus	oesophagus
18	chr8:124086600-124145200	Weak transcription	Fetal Brain Male	brain
19	chr8:124086600-124168800	Weak transcription	Lung	lung
20	chr8:124087200-124143800	Weak transcription	Fetal Kidney	kidney
21	chr8:124088600-124115800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:124089400-124116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:124095600-124118000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr8:124095800-124142800	Weak transcription	Fetal Intestine Small	intestine
25	chr8:124096200-124168800	Weak transcription	Liver	Liver
26	chr8:124096400-124118000	Weak transcription	Brain Anterior Caudate	brain
27	chr8:124096600-124115800	Weak transcription	NHLF	lung
28	chr8:124097400-124133400	Weak transcription	Left Ventricle	heart
29	chr8:124097400-124166800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr8:124098400-124166600	Weak transcription	Gastric	stomach
31	chr8:124098600-124145200	Weak transcription	HUVEC	blood vessel
32	chr8:124099000-124166800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr8:124099200-124115800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:124099200-124119400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr8:124099400-124118000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:124100000-124149800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr8:124104600-124117800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr8:124106000-124119400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr8:124107200-124114800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr8:124107200-124115000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr8:124107400-124114600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr8:124107400-124166800	Weak transcription	Pancreas	Pancrea
43	chr8:124107600-124114800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr8:124107800-124115400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr8:124107800-124116200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr8:124107800-124116200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr8:124108400-124114800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr8:124108400-124115200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:124108800-124115800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr8:124109000-124169000	Weak transcription	Fetal Heart	heart

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