Variant report

Variant	rs6468787
Chromosome Location	chr8:102712874-102712875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10093032	0.81[EUR][1000 genomes]
rs10095534	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10099953	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075791	0.91[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11782150	0.81[EUR][1000 genomes]
rs12681368	0.82[GIH][hapmap]
rs13270960	0.89[GIH][hapmap]
rs13272106	0.91[GIH][hapmap];0.81[EUR][1000 genomes]
rs13281022	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs2211920	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2387620	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2387621	0.83[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3735713	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs3735714	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs4734039	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs4734584	0.85[ASW][hapmap];0.95[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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734585	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4734587	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56306107	0.81[EUR][1000 genomes]
rs6468786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6468791	0.80[MEX][hapmap]
rs6990400	0.91[JPT][hapmap]
rs7460166	0.83[EUR][1000 genomes]
rs7825269	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7826700	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs7844804	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[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	esv3401576	chr8:102640273-102724495	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6468787	ALPK2	trans	cerebellum	SCAN
rs6468787	ODF1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102697600-102713000	Weak transcription	Psoas Muscle	Psoas
2	chr8:102699600-102714800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr8:102700000-102730600	Weak transcription	Aorta	Aorta
4	chr8:102701200-102713200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:102702000-102715600	Weak transcription	Pancreas	Pancrea
6	chr8:102702400-102713000	Weak transcription	Lung	lung
7	chr8:102703800-102713000	Weak transcription	Left Ventricle	heart
8	chr8:102704200-102713200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:102705600-102715800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr8:102706800-102713000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr8:102708800-102729000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr8:102709000-102713200	Weak transcription	Primary T cells from cord blood	blood
13	chr8:102711600-102713200	Weak transcription	Brain Anterior Caudate	brain
14	chr8:102712400-102713000	Genic enhancers	Fetal Muscle Leg	muscle
15	chr8:102712400-102713600	Enhancers	Right Ventricle	heart
16	chr8:102712400-102714000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:102712400-102714000	Enhancers	Thymus	Thymus
18	chr8:102712400-102716400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr8:102712600-102713400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr8:102712600-102713600	Enhancers	Brain Hippocampus Middle	brain
21	chr8:102712600-102713800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr8:102712600-102713800	Enhancers	Fetal Muscle Trunk	muscle
23	chr8:102712600-102713800	Enhancers	Placenta	Placenta
24	chr8:102712600-102713800	Enhancers	Fetal Stomach	stomach
25	chr8:102712600-102714000	Enhancers	Ovary	ovary
26	chr8:102712600-102714200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr8:102712600-102714200	Enhancers	Colon Smooth Muscle	Colon
28	chr8:102712600-102714200	Enhancers	Fetal Kidney	kidney
29	chr8:102712600-102714400	Enhancers	Primary hematopoietic stem cells	blood
30	chr8:102712600-102714800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr8:102712600-102714800	Enhancers	Fetal Thymus	thymus
32	chr8:102712600-102714800	Enhancers	Spleen	Spleen
33	chr8:102712600-102716600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr8:102712800-102713400	Weak transcription	Liver	Liver
35	chr8:102712800-102714000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr8:102712800-102714000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr8:102712800-102714000	Enhancers	Adipose Nuclei	Adipose
38	chr8:102712800-102714000	Flanking Active TSS	GM12878-XiMat	blood
39	chr8:102712800-102714000	Enhancers	NHDF-Ad	bronchial
40	chr8:102712800-102714600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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