Variant report

Variant	rs10194420
Chromosome Location	chr2:180115811-180115812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180115733..180117570-chr2:180124952..180126888,2	MCF-7	breast:
2	chr2:180114644..180119395-chr2:180127594..180130471,4	MCF-7	breast:
3	chr2:180114550..180116150-chr2:180123274..180125911,2	MCF-7	breast:
4	chr2:180114654..180117674-chr2:180127724..180131363,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10164707	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10164814	0.80[ASN][1000 genomes]
rs10177122	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177402	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181291	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10181464	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10182477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194534	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10196366	0.80[ASN][1000 genomes]
rs10204985	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209887	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10439300	0.88[AFR][1000 genomes]
rs10930859	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12105846	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12617002	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12621023	0.92[EUR][1000 genomes]
rs12621115	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12622075	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623243	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693179	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12693181	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693183	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12987285	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13020645	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382185	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13384403	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392996	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396340	0.85[EUR][1000 genomes]
rs13414296	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13417919	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007593	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28838656	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57098667	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433770	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67043078	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731614	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6743412	0.88[ASN][1000 genomes]
rs6759983	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7569887	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7601366	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7608745	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9288026	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10194420	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs10194420	SESTD1	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 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	chr2:180103200-180116000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:180105600-180116000	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:180105600-180120000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:180106200-180116400	Weak transcription	Small Intestine	intestine
8	chr2:180110000-180116800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:180110200-180124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:180111200-180120400	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:180112200-180120000	Weak transcription	Fetal Kidney	kidney
12	chr2:180112400-180126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:180112600-180116400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:180112600-180117600	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:180112600-180118400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:180112600-180125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix
18	chr2:180112800-180117200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:180113200-180116200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:180114200-180116800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:180114600-180116200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:180115000-180116800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:180115000-180117600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:180115200-180116800	Weak transcription	Adipose Nuclei	Adipose
25	chr2:180115200-180117800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:180115400-180116400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:180115400-180116400	Weak transcription	NHDF-Ad	bronchial
28	chr2:180115400-180116600	Weak transcription	Osteobl	bone
29	chr2:180115400-180127600	Weak transcription	NHLF	lung
30	chr2:180115600-180116000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr2:180115600-180116400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:180115800-180116200	Enhancers	Primary B cells from cord blood	blood
33	chr2:180115800-180116400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr2:180115800-180116600	Flanking Active TSS	GM12878-XiMat	blood
35	chr2:180115800-180116800	Weak transcription	HepG2	liver
36	chr2:180115800-180117600	Enhancers	Primary T cells from cord blood	blood

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