Variant report

Variant	rs300917
Chromosome Location	chr4:144269849-144269850
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:144268435..144271097-chr4:144272609..144275318,3	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10012713	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10013047	0.83[ASN][1000 genomes]
rs1027851	0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1027852	0.83[ASN][1000 genomes]
rs10519691	0.81[CHD][hapmap]
rs11100786	0.81[ASN][1000 genomes]
rs11100787	0.80[ASN][1000 genomes]
rs11100788	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11730569	0.84[ASN][1000 genomes]
rs11947952	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12647531	0.84[ASN][1000 genomes]
rs12649592	0.81[ASN][1000 genomes]
rs13101346	0.83[ASN][1000 genomes]
rs13123498	0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1397528	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs1472873	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1510880	0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1866756	0.83[ASN][1000 genomes]
rs2013856	0.84[ASN][1000 genomes]
rs2048408	0.81[ASN][1000 genomes]
rs2055730	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2119270	0.81[ASN][1000 genomes]
rs2196908	0.83[ASN][1000 genomes]
rs2196909	0.83[ASN][1000 genomes]
rs300890	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs300891	0.84[ASN][1000 genomes]
rs300892	0.85[ASN][1000 genomes]
rs300893	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs300894	0.95[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs300895	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs300899	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs300901	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs300902	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs300903	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs300904	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs300905	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs300910	0.90[ASN][1000 genomes]
rs300911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs300912	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs300913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs300914	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs300915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs300916	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs300918	0.98[ASN][1000 genomes]
rs300919	0.81[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs300943	0.95[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs300946	0.86[EUR][1000 genomes]
rs300947	0.88[EUR][1000 genomes]
rs300951	0.95[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs300953	0.88[EUR][1000 genomes]
rs3792652	0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3792653	0.81[ASN][1000 genomes]
rs3792655	0.84[ASN][1000 genomes]
rs3805238	0.89[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs3805245	0.81[ASN][1000 genomes]
rs3805246	0.84[ASN][1000 genomes]
rs3805247	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3805249	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3805251	0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3805252	0.81[ASN][1000 genomes]
rs3805253	0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3805254	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3805256	0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3805257	0.82[CEU][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3828512	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs3828513	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3828514	0.81[ASN][1000 genomes]
rs55758499	0.84[ASN][1000 genomes]
rs55894236	0.84[ASN][1000 genomes]
rs568685	0.84[ASN][1000 genomes]
rs592349	0.88[EUR][1000 genomes]
rs62337488	0.84[ASN][1000 genomes]
rs624170	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs624189	0.84[ASN][1000 genomes]
rs6537154	0.80[ASN][1000 genomes]
rs6537155	0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs666542	0.86[EUR][1000 genomes]
rs713140	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs719392	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7680959	0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs906571	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv964100	chr4:144268743-144271466	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs300917	SLC10A7	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144259200-144272400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:144259400-144272000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:144259400-144272600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:144259600-144276200	Weak transcription	Fetal Kidney	kidney
5	chr4:144260000-144272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:144261600-144272600	Weak transcription	Adipose Nuclei	Adipose
7	chr4:144263000-144276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:144263000-144277800	Weak transcription	Fetal Thymus	thymus
9	chr4:144264000-144270200	Enhancers	Rectal Smooth Muscle	rectum
10	chr4:144264000-144276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:144264600-144270000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:144265000-144270000	Enhancers	Colon Smooth Muscle	Colon
13	chr4:144265600-144270000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr4:144265600-144270200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:144265600-144272000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:144265600-144276400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:144265800-144270000	Enhancers	Brain Angular Gyrus	brain
18	chr4:144265800-144272000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:144265800-144276400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:144266200-144272200	Weak transcription	Brain Germinal Matrix	brain
21	chr4:144266800-144270400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr4:144266800-144272400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:144267400-144270200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:144267400-144272800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:144267400-144272800	Weak transcription	Osteobl	bone
26	chr4:144267600-144270200	Enhancers	Brain Cingulate Gyrus	brain
27	chr4:144267800-144272200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:144267800-144272200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:144267800-144272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:144267800-144272400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:144267800-144272600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:144267800-144272800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:144268000-144270000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:144268000-144270000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr4:144268000-144270200	Enhancers	HMEC	breast
36	chr4:144268000-144270200	Enhancers	NHEK	skin
37	chr4:144268000-144272000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:144268000-144272800	Weak transcription	HSMM	muscle
39	chr4:144268400-144270000	Enhancers	Ovary	ovary
40	chr4:144268400-144270200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:144268400-144270200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr4:144268600-144270000	Enhancers	Primary hematopoietic stem cells	blood
43	chr4:144268600-144270000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr4:144268600-144270000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:144268600-144270000	Enhancers	Fetal Intestine Large	intestine
46	chr4:144268600-144270200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:144268600-144270200	Enhancers	Esophagus	oesophagus
48	chr4:144268600-144270200	Flanking Active TSS	Fetal Heart	heart
49	chr4:144268600-144270200	Enhancers	Psoas Muscle	Psoas
50	chr4:144268600-144270200	Enhancers	Sigmoid Colon	Sigmoid Colon

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