Variant report

Variant	rs253390
Chromosome Location	chr5:74977661-74977662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:74880200..74881111-chr5:74976869..74977697,3	MCF-7	breast:
2	chr5:74804046..74805995-chr5:74976601..74978123,2	K562	blood:
3	chr5:74532317..74532921-chr5:74976842..74977712,2	K562	blood:

Variant related genes	Relation type
ENSG00000145700	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10462356	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10462521	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515213	0.82[CHD][hapmap]
rs11746063	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11748378	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166183	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563863	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563877	0.82[CHD][hapmap]
rs17649055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649248	0.82[CHD][hapmap]
rs17649266	0.82[CHD][hapmap]
rs17649350	0.82[CHD][hapmap]
rs1817869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193344	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194137	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047059	0.94[ASW][hapmap];0.91[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2291630	0.82[CHD][hapmap]
rs2307113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253388	0.86[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs253389	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34905687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797580	0.83[CEU][hapmap]
rs40059	0.85[EUR][1000 genomes]
rs41534344	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703678	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4703679	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703680	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704234	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59778668	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60134294	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60423072	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61173369	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66493518	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67054144	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67803720	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868069	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633978	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633979	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7381033	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv522003	chr5:74947435-74988369	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830353	chr5:74961520-75152609	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1797759	chr5:74973241-74984269	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs253390	TNPO1	cis	cerebellum	SCAN
rs253390	DMGDH	cis	parietal	SCAN
rs253390	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74952800-74981400	Weak transcription	Psoas Muscle	Psoas
2	chr5:74961000-74987800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:74962000-74979400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:74963000-74989800	Weak transcription	Esophagus	oesophagus
5	chr5:74964800-74989400	Weak transcription	HSMMtube	muscle
6	chr5:74965000-74978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:74965000-74979800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:74965000-74983800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:74965000-74991200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:74965000-74998000	Weak transcription	Fetal Brain Female	brain
11	chr5:74965200-75011800	Weak transcription	Brain Germinal Matrix	brain
12	chr5:74965400-74978000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:74965400-74979400	Weak transcription	Brain Anterior Caudate	brain
14	chr5:74965400-74980600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:74965400-74980800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:74965400-74981000	Weak transcription	Lung	lung
17	chr5:74965400-74997800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:74965400-75012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:74965400-75012400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:74965400-75012400	Weak transcription	Right Ventricle	heart
21	chr5:74965600-74978400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:74965600-74979400	Weak transcription	Spleen	Spleen
23	chr5:74965600-74979600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:74965600-74980800	Weak transcription	Pancreas	Pancrea
25	chr5:74965600-74998200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr5:74965600-74998200	Weak transcription	Fetal Heart	heart
27	chr5:74965600-75010400	Weak transcription	Gastric	stomach
28	chr5:74965600-75011400	Weak transcription	Small Intestine	intestine
29	chr5:74965800-74991800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr5:74966000-74979400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:74966000-74991000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:74966000-74998400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:74967200-74989600	Weak transcription	Hela-S3	cervix
34	chr5:74968800-74983400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:74968800-74983800	Weak transcription	Placenta	Placenta
36	chr5:74968800-74998400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:74969000-74991600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:74969200-74977800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:74969200-74979600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:74969400-74983200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:74970800-74981000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr5:74971000-74978000	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:74971000-74979200	Weak transcription	Ovary	ovary
44	chr5:74971000-74980800	Weak transcription	Fetal Stomach	stomach
45	chr5:74971000-74983400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:74971000-74985800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:74971000-74997600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:74971200-74978800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr5:74971200-74979400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:74971200-74979400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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