Variant report

Variant	rs10835337
Chromosome Location	chr11:3958828-3958829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3952025..3954655-chr11:3956750..3959173,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1013351	0.87[EUR][1000 genomes]
rs10500590	0.81[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10742200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767702	0.87[EUR][1000 genomes]
rs10767706	0.82[CHB][hapmap];0.89[CHD][hapmap]
rs10767713	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10767715	0.81[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10767720	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10767721	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10767723	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10767767	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs10767811	0.88[TSI][hapmap]
rs10835311	0.87[EUR][1000 genomes]
rs10835312	0.86[EUR][1000 genomes]
rs10835320	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10835324	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835331	0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10835333	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835340	0.81[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs10835359	0.86[EUR][1000 genomes]
rs10835390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835399	0.85[EUR][1000 genomes]
rs10835402	0.85[EUR][1000 genomes]
rs10835403	0.83[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs10835406	0.85[EUR][1000 genomes]
rs10835407	0.81[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs10835508	0.83[YRI][hapmap]
rs10835596	0.90[TSI][hapmap]
rs11030276	0.87[EUR][1000 genomes]
rs11030404	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11030639	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs11030781	0.90[TSI][hapmap]
rs1155146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828337	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12223176	0.86[EUR][1000 genomes]
rs12270732	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12281293	0.87[EUR][1000 genomes]
rs12283447	0.85[EUR][1000 genomes]
rs12286710	0.87[EUR][1000 genomes]
rs12290747	0.87[EUR][1000 genomes]
rs12295138	0.83[EUR][1000 genomes]
rs1349583	0.81[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs1452047	0.81[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1452048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17081	0.81[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs17279635	0.81[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs1839910	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2412338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2898947	0.86[EUR][1000 genomes]
rs4910865	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910866	0.87[EUR][1000 genomes]
rs4910868	0.86[EUR][1000 genomes]
rs4910869	0.81[GIH][hapmap];0.90[TSI][hapmap]
rs6578424	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66503725	0.86[EUR][1000 genomes]
rs66596383	0.88[EUR][1000 genomes]
rs67300156	0.88[EUR][1000 genomes]
rs7102215	0.87[EUR][1000 genomes]
rs7113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120938	0.82[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap]
rs7128762	0.87[EUR][1000 genomes]
rs720571	0.83[EUR][1000 genomes]
rs750525	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7924984	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925954	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7950153	0.80[ASW][hapmap];0.87[GIH][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs963998	0.90[TSI][hapmap]
rs995498	0.81[GIH][hapmap];0.90[TSI][hapmap];0.87[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	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv896895	chr11:3942001-3972236	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10835337	OR51E2	cis	cerebellum	SCAN
rs10835337	RRM1	cis	Thyroid	GTEx
rs10835337	RRM1	cis	cerebellum	SCAN
rs10835337	RRM1	cis	Artery Tibial	GTEx
rs10835337	RRM1	cis	parietal	SCAN
rs10835337	IFITM5	cis	cerebellum	SCAN
rs10835337	CD81	cis	parietal	SCAN
rs10835337	OR51A4	cis	parietal	SCAN
rs10835337	STIM1	cis	lung	GTEx
rs10835337	FAM160A2	cis	parietal	SCAN
rs10835337	TRIM21	cis	cerebellum	SCAN
rs10835337	ANO9	cis	parietal	SCAN
rs10835337	RRM1	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3948400-3960400	Weak transcription	NHEK	skin
2	chr11:3948800-3960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:3949000-3961400	Weak transcription	Right Atrium	heart
4	chr11:3949400-3959400	Weak transcription	Fetal Lung	lung
5	chr11:3950400-3972200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:3951000-3960600	Weak transcription	Stomach Mucosa	stomach
7	chr11:3951200-3965400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:3951200-3967600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:3951400-3959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:3951400-3959200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:3951400-3959800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:3951400-3961400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:3951400-3963400	Weak transcription	A549	lung
14	chr11:3951400-3963600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr11:3951600-3959800	Weak transcription	Adipose Nuclei	Adipose
16	chr11:3951600-3963400	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:3951800-3959600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:3952000-3963400	Weak transcription	Pancreas	Pancrea
19	chr11:3952200-3961000	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:3954000-3960400	Enhancers	Psoas Muscle	Psoas
21	chr11:3954000-3963800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr11:3954600-3959200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr11:3954800-3963200	Weak transcription	Liver	Liver
24	chr11:3955000-3960400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:3955400-3963400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr11:3955600-3962000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr11:3955800-3960800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:3955800-3963200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:3955800-3963200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:3955800-3963400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr11:3956200-3960400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:3956200-3962400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:3956200-3963400	Weak transcription	K562	blood
34	chr11:3956200-3964000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:3956600-3960000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:3956600-3960000	Weak transcription	HMEC	breast
37	chr11:3956600-3960400	Weak transcription	Aorta	Aorta
38	chr11:3956600-3961000	Weak transcription	Gastric	stomach
39	chr11:3956600-3961000	Weak transcription	Left Ventricle	heart
40	chr11:3956600-3961400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:3956600-3963000	Weak transcription	Right Ventricle	heart
42	chr11:3956600-3963400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:3956800-3960000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:3956800-3960000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:3956800-3960600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:3956800-3961000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:3956800-3962600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:3957000-3963400	Weak transcription	Colon Smooth Muscle	Colon
49	chr11:3957400-3959000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr11:3957400-3959000	Enhancers	Ovary	ovary

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