Variant report

Variant	rs17394390
Chromosome Location	chr1:45670445-45670446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45662426..45664020-chr1:45669808..45671855,2	MCF-7	breast:
2	chr1:45451641..45453252-chr1:45669605..45671686,2	MCF-7	breast:
3	chr1:45283980..45286629-chr1:45670146..45671659,2	K562	blood:
4	chr1:45665465..45667003-chr1:45668749..45671725,2	K562	blood:
5	chr1:45670063..45672201-chr1:45674093..45675823,3	K562	blood:
6	chr1:45669107..45671536-chr1:45764944..45767322,2	K562	blood:

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction
ENSG00000070785	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1502340	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938299	1.00[AFR][1000 genomes]
rs2096435	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660298	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660299	0.85[EUR][1000 genomes]
rs4660837	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58612171	0.84[EUR][1000 genomes]
rs61788378	1.00[AFR][1000 genomes]
rs61788379	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs61788380	1.00[AFR][1000 genomes]
rs61788382	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788383	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61788386	0.93[AMR][1000 genomes]
rs61788387	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788388	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788389	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61788390	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788393	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788427	0.90[AMR][1000 genomes]
rs61788428	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61788429	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788430	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788436	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788438	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788439	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789773	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789775	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61789785	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61789788	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789789	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789808	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789809	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789814	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789816	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789817	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789818	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789819	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61789820	0.85[EUR][1000 genomes]
rs61789821	0.85[EUR][1000 genomes]
rs61789822	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61789826	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61789830	1.00[AFR][1000 genomes]
rs6429564	1.00[CHB][hapmap];0.82[JPT][hapmap]

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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45660000-45670800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45668000-45673800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:45668600-45672800	Active TSS	Fetal Brain Female	brain
4	chr1:45668800-45670800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr1:45669000-45671000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:45669200-45670800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr1:45669200-45670800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:45669400-45671000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:45669400-45671200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:45669400-45673200	Active TSS	Brain Angular Gyrus	brain
11	chr1:45669400-45673400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:45669600-45670800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:45669600-45672600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:45669800-45670600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:45669800-45670800	Active TSS	HepG2	liver
16	chr1:45669800-45671000	Active TSS	Brain Germinal Matrix	brain
17	chr1:45670000-45670600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
18	chr1:45670000-45670800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
19	chr1:45670000-45672600	Active TSS	Brain Anterior Caudate	brain
20	chr1:45670000-45672600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr1:45670000-45672800	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:45670000-45673200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:45670000-45673400	Active TSS	Ovary	ovary
24	chr1:45670200-45670600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:45670200-45670600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
26	chr1:45670200-45670600	Enhancers	Fetal Intestine Small	intestine
27	chr1:45670200-45670800	Active TSS	Fetal Intestine Large	intestine
28	chr1:45670200-45671000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr1:45670200-45671200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:45670200-45671400	Active TSS	Fetal Brain Male	brain
31	chr1:45670200-45672600	Active TSS	Brain Cingulate Gyrus	brain
32	chr1:45670200-45672600	Active TSS	Brain Hippocampus Middle	brain
33	chr1:45670200-45672600	Active TSS	Duodenum Mucosa	Duodenum
34	chr1:45670200-45672800	Active TSS	Rectal Smooth Muscle	rectum
35	chr1:45670400-45671000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr1:45670400-45671200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
37	chr1:45670400-45671400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr1:45670400-45672600	Active TSS	Stomach Smooth Muscle	stomach
39	chr1:45670400-45672600	Active TSS	Hela-S3	cervix
40	chr1:45670400-45673200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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