Variant report

Variant	rs10205999
Chromosome Location	chr2:180116393-180116394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180115892..180117617-chr2:180123291..180126152,2	K562	blood:
2	chr2:180116382..180118315-chr2:180123410..180126262,2	MCF-7	breast:
3	chr2:180115733..180117570-chr2:180124952..180126888,2	MCF-7	breast:
4	chr2:180114644..180119395-chr2:180127594..180130471,4	MCF-7	breast:
5	chr2:180114654..180117674-chr2:180127724..180131363,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10170520	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10174774	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10186198	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10192426	0.83[AFR][1000 genomes]
rs10204985	0.87[AFR][1000 genomes]
rs10439299	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10930858	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158872	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884516	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11894870	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898291	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12105846	0.87[AFR][1000 genomes]
rs12997314	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13026497	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383965	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13391602	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13418701	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1374378	0.83[AFR][1000 genomes]
rs1907421	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2008999	0.83[AFR][1000 genomes]
rs2289992	0.82[AFR][1000 genomes]
rs2847	0.82[AFR][1000 genomes]
rs4585064	0.83[EUR][1000 genomes]
rs6433757	0.84[AFR][1000 genomes]
rs6433760	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433761	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433764	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433769	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707081	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734121	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736098	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6742739	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6756326	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562730	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579536	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7585600	0.83[EUR][1000 genomes]
rs7608882	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10205999	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
2	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
3	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
4	chr2:180105600-180120000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:180106200-180116400	Weak transcription	Small Intestine	intestine
6	chr2:180110000-180116800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:180110200-180124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:180111200-180120400	Enhancers	Primary B cells from peripheral blood	blood
9	chr2:180112200-180120000	Weak transcription	Fetal Kidney	kidney
10	chr2:180112400-180126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:180112600-180116400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:180112600-180117600	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:180112600-180118400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:180112600-180125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix
16	chr2:180112800-180117200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:180114200-180116800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:180115000-180116800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:180115000-180117600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:180115200-180116800	Weak transcription	Adipose Nuclei	Adipose
21	chr2:180115200-180117800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr2:180115400-180116400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:180115400-180116400	Weak transcription	NHDF-Ad	bronchial
24	chr2:180115400-180116600	Weak transcription	Osteobl	bone
25	chr2:180115400-180127600	Weak transcription	NHLF	lung
26	chr2:180115600-180116400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:180115800-180116400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:180115800-180116600	Flanking Active TSS	GM12878-XiMat	blood
29	chr2:180115800-180116800	Weak transcription	HepG2	liver
30	chr2:180115800-180117600	Enhancers	Primary T cells from cord blood	blood
31	chr2:180116000-180116400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr2:180116000-180117800	Enhancers	Stomach Smooth Muscle	stomach
33	chr2:180116000-180118000	Enhancers	Colon Smooth Muscle	Colon
34	chr2:180116200-180116400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr2:180116200-180116400	Enhancers	Aorta	Aorta
36	chr2:180116200-180116800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:180116200-180117800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:180116200-180117800	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr2:180116200-180118200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:180116200-180118400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:180116200-180118600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr2:180116200-180124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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