Variant report

Variant	rs10047168
Chromosome Location	chr1:169343533-169343534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169337001..169338585-chr1:169341671..169343968,2	MCF-7	breast:
2	chr1:169341801..169344771-chr1:169346777..169350780,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117475	Chromatin interaction
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10800430	1.00[EUR][1000 genomes]
rs10800436	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800443	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800445	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919079	0.82[EUR][1000 genomes]
rs10919097	0.82[EUR][1000 genomes]
rs10919098	0.82[EUR][1000 genomes]
rs10919100	0.82[EUR][1000 genomes]
rs10919104	0.82[EUR][1000 genomes]
rs10919111	0.82[EUR][1000 genomes]
rs10919131	0.91[EUR][1000 genomes]
rs10919151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919152	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919157	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919159	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11487548	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11805562	1.00[EUR][1000 genomes]
rs11807896	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11810815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12058325	1.00[EUR][1000 genomes]
rs12059944	0.85[ASN][1000 genomes]
rs12061069	0.97[EUR][1000 genomes]
rs12061080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12061405	0.82[EUR][1000 genomes]
rs12063056	0.97[EUR][1000 genomes]
rs12063719	0.97[EUR][1000 genomes]
rs12063863	0.97[EUR][1000 genomes]
rs12065030	1.00[EUR][1000 genomes]
rs12067139	0.97[EUR][1000 genomes]
rs12067351	1.00[EUR][1000 genomes]
rs12070031	0.82[EUR][1000 genomes]
rs12071630	0.94[ASN][1000 genomes]
rs12073439	1.00[EUR][1000 genomes]
rs12074013	0.82[EUR][1000 genomes]
rs12074966	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12076519	1.00[EUR][1000 genomes]
rs12081030	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12081562	0.82[EUR][1000 genomes]
rs12088672	0.97[EUR][1000 genomes]
rs12091133	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12091844	0.89[ASN][1000 genomes]
rs12092506	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12092952	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12094791	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12097260	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12097682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12561922	0.97[EUR][1000 genomes]
rs12565852	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280257	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737683	0.89[ASN][1000 genomes]
rs3753298	0.82[EUR][1000 genomes]
rs3765227	0.89[ASN][1000 genomes]
rs3766064	0.82[EUR][1000 genomes]
rs3766082	0.82[EUR][1000 genomes]
rs3766088	1.00[EUR][1000 genomes]
rs3766092	1.00[EUR][1000 genomes]
rs3820057	0.82[EUR][1000 genomes]
rs41272453	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57776592	0.97[EUR][1000 genomes]
rs60011235	0.97[EUR][1000 genomes]
rs7515326	0.97[EUR][1000 genomes]
rs7544446	0.97[EUR][1000 genomes]
rs9628661	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169351200	Weak transcription	Lung	lung
2	chr1:169338000-169351200	Weak transcription	Spleen	Spleen
3	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
4	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
5	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
6	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:169338000-169365200	Weak transcription	Gastric	stomach
8	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
9	chr1:169338200-169345800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:169338200-169345800	Weak transcription	Ovary	ovary
11	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
17	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:169338400-169345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:169338400-169345800	Weak transcription	Right Ventricle	heart
20	chr1:169338400-169349600	Weak transcription	HSMMtube	muscle
21	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:169338600-169345800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:169338600-169345800	Weak transcription	Colonic Mucosa	Colon
25	chr1:169338600-169345800	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:169338600-169345800	Weak transcription	Psoas Muscle	Psoas
27	chr1:169338600-169346000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:169338600-169346000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:169338600-169349800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:169338600-169351400	Weak transcription	Thymus	Thymus
31	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
32	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
33	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
34	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:169338800-169345800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:169338800-169347400	Weak transcription	Fetal Brain Female	brain
38	chr1:169339000-169344200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:169339200-169343800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:169339200-169343800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:169339200-169345600	Weak transcription	A549	lung
42	chr1:169339200-169351800	Weak transcription	Fetal Brain Male	brain
43	chr1:169339400-169344400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:169339400-169345600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:169339400-169345800	Weak transcription	HepG2	liver
46	chr1:169339400-169346000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:169339400-169347600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:169339600-169345200	Weak transcription	Brain Angular Gyrus	brain
49	chr1:169339600-169345800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:169339600-169345800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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