Variant report

Variant	rs10249931
Chromosome Location	chr7:26872142-26872143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10215738	0.81[AFR][1000 genomes]
rs10225700	0.87[AFR][1000 genomes]
rs10225924	0.82[AFR][1000 genomes]
rs10227231	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs10227529	0.87[AFR][1000 genomes]
rs10227673	0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs10236221	0.89[AFR][1000 genomes]
rs10242572	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs10244986	0.84[AFR][1000 genomes]
rs10248500	0.86[AFR][1000 genomes]
rs10251839	0.89[AFR][1000 genomes]
rs10252275	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10256250	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs10259983	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10267950	0.82[AFR][1000 genomes]
rs10270187	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10272190	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs10272303	0.82[AFR][1000 genomes]
rs10272457	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs10272603	0.89[AFR][1000 genomes]
rs10275896	0.81[AFR][1000 genomes]
rs10280476	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10281933	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10486483	0.87[YRI][hapmap];0.87[AFR][1000 genomes]
rs10486484	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10486485	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs12532199	0.83[AFR][1000 genomes]
rs12532395	0.82[AFR][1000 genomes]
rs12534899	0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs12534921	0.87[AFR][1000 genomes]
rs12535784	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs12536145	0.87[AFR][1000 genomes]
rs12536560	0.84[AFR][1000 genomes]
rs12537323	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs12540045	0.86[AFR][1000 genomes]
rs12540508	0.89[AFR][1000 genomes]
rs13438513	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs13438514	0.87[YRI][hapmap]
rs17154529	0.86[YRI][hapmap];0.88[AFR][1000 genomes]
rs17315334	0.81[AFR][1000 genomes]
rs17315775	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs17315929	0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs17375272	0.86[AFR][1000 genomes]
rs1967332	0.90[AFR][1000 genomes]
rs2030133	0.80[AFR][1000 genomes]
rs2030134	0.80[AFR][1000 genomes]
rs2030136	0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs2031811	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs28404962	0.81[AFR][1000 genomes]
rs28550029	0.90[AFR][1000 genomes]
rs28816386	0.82[AFR][1000 genomes]
rs28883078	0.89[AFR][1000 genomes]
rs3213853	0.87[AFR][1000 genomes]
rs3801803	0.84[AFR][1000 genomes]
rs3801805	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs3801807	0.87[YRI][hapmap];0.87[AFR][1000 genomes]
rs3801808	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs3801809	0.87[AFR][1000 genomes]
rs3801810	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs3801812	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs3801813	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs3801814	0.90[AFR][1000 genomes]
rs3801815	0.85[AFR][1000 genomes]
rs3801816	0.90[AFR][1000 genomes]
rs3801820	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801821	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801822	0.83[AFR][1000 genomes]
rs3801825	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801826	0.83[AFR][1000 genomes]
rs3801827	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801828	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801829	0.83[AFR][1000 genomes]
rs3801830	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs3801831	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801832	0.83[AFR][1000 genomes]
rs3801833	0.83[AFR][1000 genomes]
rs3801834	0.83[AFR][1000 genomes]
rs3801837	0.83[AFR][1000 genomes]
rs3801840	0.81[AFR][1000 genomes]
rs3801850	0.82[AFR][1000 genomes]
rs3823928	0.87[AFR][1000 genomes]
rs3823930	0.83[AFR][1000 genomes]
rs3823931	0.83[AFR][1000 genomes]
rs3823932	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs3823933	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs3823936	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs3823938	0.83[AFR][1000 genomes]
rs3934268	0.87[AFR][1000 genomes]
rs4719882	0.81[AFR][1000 genomes]
rs4722644	0.81[AFR][1000 genomes]
rs4722647	0.87[AFR][1000 genomes]
rs55739485	0.83[AFR][1000 genomes]
rs56154570	0.89[AFR][1000 genomes]
rs57135974	0.83[AFR][1000 genomes]
rs58760954	0.83[AFR][1000 genomes]
rs59254259	0.83[AFR][1000 genomes]
rs61354389	0.89[AFR][1000 genomes]
rs6461980	0.87[AFR][1000 genomes]
rs6944926	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6948657	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs73067435	0.83[AFR][1000 genomes]
rs73067443	0.83[AFR][1000 genomes]
rs73067456	0.81[AFR][1000 genomes]
rs73067475	0.83[AFR][1000 genomes]
rs73067476	0.83[AFR][1000 genomes]
rs73067479	0.80[AFR][1000 genomes]
rs73069507	0.89[AFR][1000 genomes]
rs73069510	0.89[AFR][1000 genomes]
rs7785689	0.80[AFR][1000 genomes]
rs7785798	0.83[AFR][1000 genomes]
rs7785815	0.82[AFR][1000 genomes]
rs7785832	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs7785918	0.81[AFR][1000 genomes]
rs7789225	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7791513	0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs7802715	0.81[AFR][1000 genomes]
rs7804356	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs7804620	0.87[AFR][1000 genomes]
rs7805766	0.88[YRI][hapmap];0.86[AFR][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	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv887855	chr7:26823963-26872652	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:26853400-26882600	Weak transcription	Adipose Nuclei	Adipose
3	chr7:26854200-26876400	Weak transcription	Fetal Lung	lung
4	chr7:26860600-26875400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:26861000-26882600	Weak transcription	HUVEC	blood vessel
6	chr7:26861200-26876600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:26862200-26877800	Weak transcription	Primary T cells from cord blood	blood
8	chr7:26862600-26872800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr7:26863200-26893200	Weak transcription	A549	lung
10	chr7:26863600-26894600	Weak transcription	Fetal Intestine Large	intestine
11	chr7:26863800-26872400	Weak transcription	Esophagus	oesophagus
12	chr7:26867200-26897000	Weak transcription	Lung	lung
13	chr7:26868800-26872800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr7:26869200-26889800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:26870000-26884200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:26870000-26885000	Weak transcription	GM12878-XiMat	blood
17	chr7:26870400-26894400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:26870600-26872800	Strong transcription	Primary B cells from cord blood	blood
19	chr7:26870600-26896000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr7:26871000-26902200	Weak transcription	Dnd41	blood
21	chr7:26871200-26872600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:26871400-26872200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:26871400-26872400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:26871400-26872600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr7:26871400-26872600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr7:26871400-26872600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr7:26871400-26872800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:26871400-26873200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:26871600-26872200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:26871600-26872200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr7:26871600-26896000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:26871800-26872600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:26871800-26872800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:26872000-26872400	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr7:26872000-26872400	Enhancers	HMEC	breast
36	chr7:26872000-26872600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr7:26872000-26872600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:26872000-26872600	Enhancers	NHEK	skin
39	chr7:26872000-26875800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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