Variant report

Variant	rs7916104
Chromosome Location	chr10:27093333-27093334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:27089103..27090816-chr10:27092531..27095480,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10508721	0.86[LWK][hapmap];0.90[YRI][hapmap]
rs12413383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12764628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12774231	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12776877	0.87[EUR][1000 genomes]
rs12779919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12780703	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16927334	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17669895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17747961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17748178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2018904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094150	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2182294	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2182295	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35175791	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531360	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5010875	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5025734	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67940790	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs68021348	0.84[EUR][1000 genomes]
rs7091364	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7092950	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7096584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7920164	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv933544	chr10:27005220-27111998	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv947600	chr10:27090659-27093432	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7916104	PDSS1	cis	cerebellum	SCAN
rs7916104	TPRT	cis	multi-tissue	Pritchard
rs7916104	LYZL2	cis	parietal	SCAN
rs7916104	ABI1	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27075000-27104600	Weak transcription	Esophagus	oesophagus
2	chr10:27082200-27105400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:27082600-27094000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:27083600-27094800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:27085600-27119000	Weak transcription	Fetal Lung	lung
6	chr10:27085800-27095600	Enhancers	Primary B cells from peripheral blood	blood
7	chr10:27086000-27093400	Weak transcription	Fetal Intestine Small	intestine
8	chr10:27086200-27096600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr10:27086600-27110400	Weak transcription	Fetal Intestine Large	intestine
10	chr10:27087000-27097000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:27087200-27094400	Weak transcription	Aorta	Aorta
12	chr10:27087200-27096800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr10:27088000-27096000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr10:27088200-27093400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr10:27088200-27100800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr10:27088400-27096800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr10:27088600-27098800	Weak transcription	Pancreas	Pancrea
18	chr10:27089000-27095600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr10:27090000-27093800	Enhancers	Dnd41	blood
20	chr10:27090000-27096400	Weak transcription	Fetal Stomach	stomach
21	chr10:27090200-27093600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr10:27090200-27094000	Weak transcription	Right Atrium	heart
23	chr10:27090400-27095200	Weak transcription	Lung	lung
24	chr10:27090400-27097400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr10:27090600-27094000	Enhancers	Primary T cells from cord blood	blood
26	chr10:27090600-27096800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr10:27091400-27093400	Enhancers	Primary B cells from cord blood	blood
28	chr10:27091400-27093400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr10:27091400-27095200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr10:27091400-27095200	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr10:27091400-27095400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr10:27091400-27095600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr10:27091400-27095600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr10:27091400-27095800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr10:27091600-27093600	Enhancers	Primary hematopoietic stem cells	blood
36	chr10:27091600-27094200	Enhancers	Stomach Mucosa	stomach
37	chr10:27091600-27095600	Enhancers	Thymus	Thymus
38	chr10:27091800-27094400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:27091800-27113200	Weak transcription	Placenta	Placenta
40	chr10:27092000-27093400	Enhancers	Adipose Nuclei	Adipose
41	chr10:27092000-27094000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr10:27092000-27094000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr10:27092000-27094000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:27092000-27094000	Weak transcription	Psoas Muscle	Psoas
45	chr10:27092000-27094600	Weak transcription	Spleen	Spleen
46	chr10:27092000-27095000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:27092000-27095600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:27092200-27093400	Weak transcription	Brain Anterior Caudate	brain
49	chr10:27092200-27093800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr10:27092200-27094000	Weak transcription	Brain Cingulate Gyrus	brain

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