Variant report

Variant	rs286153
Chromosome Location	chr5:59928948-59928949
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	POLR2A	chr5:59926595-59929254	K562	blood:	n/a	n/a
2	CTCF	chr5:59928920-59929070	BJ	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:59922141..59924834-chr5:59928114..59930077,2	K562	blood:
2	chr5:59928659..59931200-chr5:59937344..59939413,2	K562	blood:
3	chr5:59928143..59930570-chr5:60056842..60058406,2	MCF-7	breast:

Variant related genes	Relation type
DEPDC1B	TF binding region
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10043291	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10058456	0.95[CHB][hapmap];0.92[JPT][hapmap]
rs10805370	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs10939855	0.87[ASN][1000 genomes]
rs10939856	0.88[ASN][1000 genomes]
rs10939857	0.87[EUR][1000 genomes]
rs10939860	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs10939862	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs11739209	0.87[EUR][1000 genomes]
rs11739724	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11740327	0.85[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs11741754	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs11745077	0.88[EUR][1000 genomes]
rs11745627	0.84[EUR][1000 genomes]
rs11747927	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11948543	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11951503	0.97[ASN][1000 genomes]
rs11951950	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11952735	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11955398	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs11956023	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11959922	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12514253	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs12515025	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs12517174	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs12517207	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs12522801	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12655515	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs1379114	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs1379115	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1379116	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1379117	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1444237	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs1445852	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1456742	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1456743	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1460958	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs1562235	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17387940	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs1816899	0.84[EUR][1000 genomes]
rs1867702	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1870014	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs1992612	0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs2045356	1.00[CEU][hapmap]
rs2061250	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206789	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs2198865	0.96[ASN][1000 genomes]
rs2409792	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs249070	0.87[ASN][1000 genomes]
rs2591636	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs286148	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs286154	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs286155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286156	0.94[ASN][1000 genomes]
rs286158	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs2898287	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34395679	0.88[EUR][1000 genomes]
rs3857236	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3958943	0.89[ASN][1000 genomes]
rs4277863	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4353978	0.86[EUR][1000 genomes]
rs4524466	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4538567	0.90[EUR][1000 genomes]
rs4699959	0.82[ASN][1000 genomes]
rs4700378	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4700379	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700380	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700381	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5012862	0.86[ASN][1000 genomes]
rs55720622	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55768631	0.89[ASN][1000 genomes]
rs56137970	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56166952	0.94[ASN][1000 genomes]
rs56191602	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59155887	0.95[ASN][1000 genomes]
rs62372964	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62373024	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62373025	0.84[EUR][1000 genomes]
rs6449483	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs6449493	0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs6874072	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs6877561	0.94[ASN][1000 genomes]
rs6896942	0.84[ASN][1000 genomes]
rs755077	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7719726	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[TSI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7720233	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7730342	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs897672	0.89[CEU][hapmap];0.96[YRI][hapmap]
rs9942410	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
2	chr5:59920400-59939800	Weak transcription	HSMM	muscle
3	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
4	chr5:59922000-59930200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:59923400-59931800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:59923400-59939800	Weak transcription	K562	blood
7	chr5:59923600-59931200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:59923800-59933400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:59924200-59929400	Strong transcription	Placenta	Placenta
10	chr5:59924400-59930200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:59924400-59941800	Weak transcription	Fetal Brain Female	brain
12	chr5:59924600-59930400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:59924600-59936200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:59924800-59929400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:59924800-59929400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:59924800-59930200	Strong transcription	HepG2	liver
17	chr5:59924800-59936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:59925000-59930000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:59925000-59942800	Strong transcription	Dnd41	blood
20	chr5:59925200-59947200	Weak transcription	Pancreas	Pancrea
21	chr5:59925400-59929000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:59925400-59929000	Weak transcription	NHLF	lung
23	chr5:59925800-59929600	Strong transcription	Fetal Thymus	thymus
24	chr5:59926000-59929000	Strong transcription	NHEK	skin
25	chr5:59926000-59929400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr5:59926000-59929400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:59926000-59929400	Strong transcription	Fetal Intestine Small	intestine
28	chr5:59926000-59929800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:59926000-59933800	Strong transcription	Fetal Intestine Large	intestine
30	chr5:59926200-59929000	Weak transcription	NHDF-Ad	bronchial
31	chr5:59926200-59929200	Strong transcription	Fetal Stomach	stomach
32	chr5:59926200-59929400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:59926200-59933400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:59926400-59929800	Weak transcription	Gastric	stomach
35	chr5:59926400-59967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:59926600-59930200	Strong transcription	Thymus	Thymus
37	chr5:59926600-59946200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:59926800-59929600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr5:59926800-59930800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:59927000-59929400	Enhancers	Aorta	Aorta
41	chr5:59927200-59944000	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:59927400-59929600	Strong transcription	A549	lung
43	chr5:59927400-59930600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:59927400-59931400	Weak transcription	Primary B cells from cord blood	blood
45	chr5:59927400-59933000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr5:59927400-59935200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:59927400-59941200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:59927600-59929200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:59927600-59933000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:59928200-59929400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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