Variant report

Variant	rs10750790
Chromosome Location	chr11:66582210-66582211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66561937..66563631-chr11:66581137..66583899,2	MCF-7	breast:
2	chr11:66444991..66446742-chr11:66580596..66582940,2	MCF-7	breast:
3	chr11:66509258..66512699-chr11:66579656..66583636,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173715	Chromatin interaction
ENSG00000173914	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10160758	0.85[ASW][hapmap];0.86[CEU][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes]
rs10791889	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10791890	0.87[EUR][1000 genomes]
rs10791891	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10791892	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896135	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896139	0.95[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11227610	0.87[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11600959	0.93[ASW][hapmap];0.90[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2077432	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2167457	0.86[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2187041	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741194	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3741364	1.00[ASW][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs4576826	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930184	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930390	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[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs551708	0.83[CEU][hapmap]
rs6591222	0.95[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7103627	0.86[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7119426	0.95[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7120256	0.95[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs714766	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7930203	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[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948839	0.90[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9971487	0.82[EUR][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	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv508638	chr11:66541653-66643634	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10750790	EHBP1L1	cis	cerebellum	SCAN
rs10750790	B3GNT1	cis	parietal	SCAN
rs10750790	CTSF	cis	Whole Blood	GTEx
rs10750790	C11orf80	cis	cerebellum	SCAN
rs10750790	VEGFB	cis	cerebellum	SCAN
rs10750790	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs10750790	KDM2A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66513400-66606800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:66527000-66595600	Weak transcription	HSMM	muscle
3	chr11:66530000-66605400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:66530200-66582400	Weak transcription	HUVEC	blood vessel
5	chr11:66530600-66600000	Weak transcription	Fetal Muscle Leg	muscle
6	chr11:66544000-66609600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:66554600-66605800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:66556200-66603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:66556600-66583600	Weak transcription	Fetal Stomach	stomach
10	chr11:66556600-66586000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:66556800-66589200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:66556800-66607400	Weak transcription	Fetal Lung	lung
13	chr11:66557200-66582400	Weak transcription	NHEK	skin
14	chr11:66558000-66583000	Weak transcription	Hela-S3	cervix
15	chr11:66560400-66595600	Weak transcription	A549	lung
16	chr11:66560400-66605400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:66561600-66609400	Weak transcription	Colonic Mucosa	Colon
18	chr11:66565000-66605400	Weak transcription	Gastric	stomach
19	chr11:66567000-66601600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr11:66567000-66606800	Weak transcription	Brain Anterior Caudate	brain
21	chr11:66567000-66609800	Weak transcription	Ovary	ovary
22	chr11:66567200-66584400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:66567400-66595600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:66568000-66609400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:66568800-66609600	Weak transcription	Fetal Kidney	kidney
26	chr11:66569800-66600000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:66570000-66605400	Weak transcription	HSMMtube	muscle
28	chr11:66570000-66606800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:66571000-66586600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:66571000-66609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:66571600-66609600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:66571800-66605400	Weak transcription	Lung	lung
33	chr11:66572000-66606600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:66572000-66609200	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:66572400-66585600	Weak transcription	Primary T cells from cord blood	blood
36	chr11:66572600-66597400	Weak transcription	Fetal Heart	heart
37	chr11:66573200-66590000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:66573200-66593200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:66573800-66595600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:66575200-66595000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr11:66576000-66582600	Weak transcription	Primary B cells from cord blood	blood
42	chr11:66576000-66583200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:66576000-66583800	Weak transcription	Brain Germinal Matrix	brain
44	chr11:66576000-66585600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:66576000-66590000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:66576000-66592400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:66576000-66605400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr11:66576000-66609600	Weak transcription	Esophagus	oesophagus
49	chr11:66576000-66609800	Weak transcription	Aorta	Aorta
50	chr11:66576200-66605200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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