Variant report

Variant	rs10275799
Chromosome Location	chr7:70597522-70597523
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10234969	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10950241	0.88[EUR][1000 genomes]
rs10950242	0.83[EUR][1000 genomes]
rs11761326	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12669913	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13245797	0.81[EUR][1000 genomes]
rs2057941	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057942	0.90[EUR][1000 genomes]
rs2867037	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867038	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867039	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903457	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2903458	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903459	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324824	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4527772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5008001	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460640	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6950440	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951608	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955782	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962253	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7783769	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs7810849	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847723	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847724	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847725	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886739	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1034662	chr7:70275712-70722953	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3406129	chr7:70595641-70598589	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	esv3377653	chr7:70596541-70599389	Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10275799	WBSCR17	cis	parietal	SCAN
rs10275799	ST13P4	trans	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70595800-70597800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr7:70595800-70597800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr7:70595800-70598600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:70595800-70598800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr7:70595800-70598800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:70595800-70599000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:70595800-70599400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr7:70595800-70599600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr7:70596000-70597600	Active TSS	HSMMtube	muscle
10	chr7:70596000-70598000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:70596000-70598000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
12	chr7:70596000-70598200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:70596000-70598200	Active TSS	Psoas Muscle	Psoas
14	chr7:70596000-70598400	Active TSS	Aorta	Aorta
15	chr7:70596000-70598400	Active TSS	Colon Smooth Muscle	Colon
16	chr7:70596000-70598400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
17	chr7:70596000-70598400	Active TSS	Fetal Kidney	kidney
18	chr7:70596000-70598600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:70596000-70598600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:70596000-70598600	Active TSS	Ovary	ovary
21	chr7:70596000-70598600	Active TSS	Right Atrium	heart
22	chr7:70596000-70598800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
23	chr7:70596000-70598800	Active TSS	Rectal Smooth Muscle	rectum
24	chr7:70596000-70599000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr7:70596000-70599200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:70596000-70599200	Active TSS	Left Ventricle	heart
27	chr7:70596000-70599400	Active TSS	Brain Anterior Caudate	brain
28	chr7:70596000-70599600	Active TSS	Brain Angular Gyrus	brain
29	chr7:70596200-70597600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:70596200-70597800	Active TSS	Gastric	stomach
31	chr7:70596200-70598000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr7:70596200-70598200	Enhancers	Liver	Liver
33	chr7:70596200-70598200	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr7:70596200-70598400	Bivalent/Poised TSS	Thymus	Thymus
35	chr7:70596200-70598600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:70596200-70599000	Active TSS	Esophagus	oesophagus
37	chr7:70596200-70599200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
38	chr7:70596400-70597800	Active TSS	Duodenum Mucosa	Duodenum
39	chr7:70596400-70597800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
40	chr7:70596400-70598200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
41	chr7:70596400-70598200	ZNF genes & repeats	Spleen	Spleen
42	chr7:70596400-70598600	Bivalent/Poised TSS	Fetal Stomach	stomach
43	chr7:70596600-70597600	Active TSS	Colonic Mucosa	Colon
44	chr7:70596600-70598200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:70596600-70598600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr7:70596800-70597800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr7:70596800-70598000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:70596800-70598200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
49	chr7:70596800-70599000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr7:70596800-70599400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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