Variant report

Variant	rs10899415
Chromosome Location	chr11:77623873-77623874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:77623595-77623917	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
INTS4	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10899417	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10899419	0.83[EUR][1000 genomes]
rs11237336	0.80[ASN][1000 genomes]
rs11534589	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11559637	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11601908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs11820337	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs11823006	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs12786047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12789522	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12796422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12801444	0.85[EUR][1000 genomes]
rs12807406	0.87[CHD][hapmap]
rs1790238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790244	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1790256	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790258	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793329	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1793331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793338	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1793344	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2186562	0.82[CEU][hapmap]
rs2187564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs2276349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2510964	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2511454	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3018156	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3018158	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3018167	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3018411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs616354	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs650636	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs6592748	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6592751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs682324	0.82[CEU][hapmap];0.83[YRI][hapmap]
rs7115539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7119390	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7120314	0.85[EUR][1000 genomes]
rs7124835	0.85[EUR][1000 genomes]
rs7932547	0.82[CEU][hapmap]
rs7939854	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7950529	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9704476	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv972897	chr11:77622081-77628075	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10899415	INTS4	cis	cerebellum	SCAN
rs10899415	THRSP	cis	cerebellum	SCAN
rs10899415	RSF1	cis	cerebellum	SCAN
rs10899415	OR2AT4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
2	chr11:77579200-77625000	Weak transcription	HMEC	breast
3	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
5	chr11:77586600-77625000	Weak transcription	Stomach Mucosa	stomach
6	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
8	chr11:77593800-77625000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr11:77597400-77625000	Weak transcription	A549	lung
11	chr11:77597600-77629400	Weak transcription	Brain Germinal Matrix	brain
12	chr11:77597800-77624800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:77597800-77625000	Weak transcription	Colon Smooth Muscle	Colon
14	chr11:77597800-77625000	Weak transcription	Pancreas	Pancrea
15	chr11:77597800-77625000	Weak transcription	NHDF-Ad	bronchial
16	chr11:77597800-77625200	Weak transcription	NHEK	skin
17	chr11:77597800-77625600	Weak transcription	HSMM	muscle
18	chr11:77597800-77629000	Weak transcription	Aorta	Aorta
19	chr11:77597800-77633800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:77597800-77644200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:77597800-77644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
24	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
27	chr11:77597800-77690000	Weak transcription	Gastric	stomach
28	chr11:77601800-77629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:77602000-77640600	Weak transcription	K562	blood
30	chr11:77602600-77625200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:77602600-77644200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr11:77603000-77625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:77603000-77637400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:77603200-77625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:77603200-77625000	Weak transcription	Osteobl	bone
37	chr11:77603200-77650200	Weak transcription	Fetal Brain Female	brain
38	chr11:77603400-77625000	Weak transcription	HUVEC	blood vessel
39	chr11:77604200-77625000	Weak transcription	NHLF	lung
40	chr11:77604600-77625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:77604800-77644200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:77605800-77624800	Weak transcription	Hela-S3	cervix
43	chr11:77610600-77625000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr11:77612600-77637000	Weak transcription	Brain Anterior Caudate	brain
45	chr11:77614600-77629200	Weak transcription	Lung	lung
46	chr11:77614800-77638800	Weak transcription	Brain Angular Gyrus	brain
47	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
48	chr11:77615000-77624800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr11:77615000-77625000	Weak transcription	Ovary	ovary
50	chr11:77615000-77644200	Weak transcription	Spleen	Spleen

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