Variant report

Variant	rs2868917
Chromosome Location	chr4:85500201-85500202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr4:85499598-85500256	HCT-116	colon:	n/a	n/a
2	CTCF	chr4:85500140-85500290	HRPEpiC	eye:	n/a	n/a
3	CTCF	chr4:85499566-85500288	A549	lung:	n/a	n/a
4	RAD21	chr4:85499667-85500243	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr4:85499726-85500211	HCT-116	colon:	n/a	n/a
6	RAD21	chr4:85499577-85500251	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr4:85499556-85500288	SK-N-SH	brain:	n/a	n/a
8	JUN	chr4:85499745-85500221	K562	blood:	n/a	n/a
9	RAD21	chr4:85499568-85500319	HCT-116	colon:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:85493510..85497718-chr4:85498470..85501665,5	MCF-7	breast:
2	chr4:85500062..85502181-chr4:85502250..85504824,3	MCF-7	breast:
3	chr4:85483371..85486524-chr4:85499401..85503831,3	MCF-7	breast:

No data

Variant related genes	Relation type
CDS1	TF binding region
ENSG00000163624	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1020278	0.83[MEX][hapmap]
rs10776519	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11097023	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11099651	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099652	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11099653	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11725539	0.82[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11733870	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11929910	0.83[JPT][hapmap]
rs12509774	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12648523	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13102661	0.83[MEX][hapmap]
rs1372971	0.83[MEX][hapmap]
rs2868914	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2868915	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2868916	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2868919	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs2868920	0.83[ASW][hapmap];0.85[CEU][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap]
rs35227341	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35909314	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4449405	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4533768	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535544	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6829806	0.83[MEX][hapmap]
rs7657036	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7657224	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7659340	0.83[JPT][hapmap]
rs7677285	0.82[JPT][hapmap];0.86[AMR][1000 genomes]
rs7678268	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699871	0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2868917	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85489800-85503400	Weak transcription	Lung	lung
2	chr4:85490000-85500400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:85490600-85500600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:85490600-85501200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:85495600-85500400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:85495600-85503400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:85495600-85503400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:85495800-85502200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:85495800-85503400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:85499200-85502400	Weak transcription	Fetal Intestine Small	intestine
11	chr4:85500000-85500600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:85500000-85500800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr4:85500000-85500800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:85500000-85501000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr4:85500000-85501000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr4:85500000-85501000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:85500000-85501000	Enhancers	Fetal Kidney	kidney
18	chr4:85500000-85501000	Enhancers	HMEC	breast
19	chr4:85500000-85501400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr4:85500200-85500600	Enhancers	NHDF-Ad	bronchial
21	chr4:85500200-85500800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:85500200-85500800	Enhancers	Fetal Heart	heart
23	chr4:85500200-85501000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr4:85500200-85501000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:85500200-85501000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr4:85500200-85501000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:85500200-85501000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:85500200-85501000	Enhancers	NHEK	skin
29	chr4:85500200-85501400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr4:85500200-85501400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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