Variant report

Variant	rs159754
Chromosome Location	chr5:36995576-36995577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr5:36995437-36995617	K562	blood:	n/a	n/a

Variant related genes	Relation type
NIPBL	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10041439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10044651	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10053695	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10056607	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10214226	1.00[MEX][hapmap]
rs10223124	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11956853	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1389861	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs149459	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap]
rs150537	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs159750	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs159911	1.00[AMR][1000 genomes]
rs159912	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28408500	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294691	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs297538	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs298970	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs300047	0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs300048	1.00[AMR][1000 genomes]
rs300056	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs300057	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs300059	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs301858	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs301900	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs391366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs463041	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55786650	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59774526	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6863784	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73750906	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73750908	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7702256	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7724311	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7735990	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9292646	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9764719	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv1023362	chr5:36927652-37010749	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv1017947	chr5:36927652-37017180	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
10	nsv1029936	chr5:36927652-37025871	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
11	nsv1029319	chr5:36928654-37017180	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
12	nsv1030883	chr5:36932448-37039857	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
13	esv1803659	chr5:36935129-37039857	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
14	nsv1033928	chr5:36947293-37039857	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
15	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv881592	chr5:36954812-37027258	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
17	esv1802391	chr5:36958598-37242600	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
18	nsv881136	chr5:36976160-37029885	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36948600-36996600	Weak transcription	HSMMtube	muscle
2	chr5:36949600-37086800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:36951400-37004400	Weak transcription	Right Ventricle	heart
4	chr5:36954400-37026400	Weak transcription	Pancreas	Pancrea
5	chr5:36954800-37023600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:36955400-37010400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:36959400-36996800	Weak transcription	Gastric	stomach
8	chr5:36962400-37028400	Weak transcription	Spleen	Spleen
9	chr5:36965800-37018600	Weak transcription	Psoas Muscle	Psoas
10	chr5:36966000-36998800	Weak transcription	Fetal Heart	heart
11	chr5:36968800-36996200	Weak transcription	Lung	lung
12	chr5:36968800-37031200	Weak transcription	Aorta	Aorta
13	chr5:36969800-37065000	Weak transcription	Stomach Mucosa	stomach
14	chr5:36972600-37019200	Weak transcription	Brain Angular Gyrus	brain
15	chr5:36974200-36996400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:36976400-36996200	Weak transcription	Brain Substantia Nigra	brain
17	chr5:36976400-37010600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:36976600-37008800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:36976600-37019200	Weak transcription	NHLF	lung
20	chr5:36976600-37022800	Weak transcription	Fetal Brain Male	brain
21	chr5:36977000-36996000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:36977000-37002000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:36977000-37003400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:36978000-36995800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:36978000-37004400	Weak transcription	Fetal Intestine Small	intestine
26	chr5:36978200-37004200	Weak transcription	Fetal Brain Female	brain
27	chr5:36979000-37002200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:36979800-37057800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:36982200-36995800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:36983000-37000400	Weak transcription	HMEC	breast
31	chr5:36983800-36999400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:36984200-36996400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:36985400-37008800	Weak transcription	Brain Germinal Matrix	brain
34	chr5:36985600-36995800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:36985800-36996000	Weak transcription	A549	lung
36	chr5:36985800-36996200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:36985800-36996400	Weak transcription	Esophagus	oesophagus
38	chr5:36985800-36999000	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:36986000-36995800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr5:36986000-36995800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:36986000-36996200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:36986000-36996200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:36986000-36996200	Weak transcription	Left Ventricle	heart
44	chr5:36986000-36996400	Weak transcription	Thymus	Thymus
45	chr5:36986000-36996600	Weak transcription	NH-A	brain
46	chr5:36986000-36999400	Weak transcription	Osteobl	bone
47	chr5:36986000-36999600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:36986000-37000200	Weak transcription	Fetal Lung	lung
49	chr5:36986000-37000200	Weak transcription	HUVEC	blood vessel
50	chr5:36986000-37001000	Weak transcription	HepG2	liver

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