Variant report

Variant	rs6533951
Chromosome Location	chr4:79644279-79644280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79639723..79644751-chr4:79695809..79700449,7	K562	blood:
2	chr4:79529076..79531360-chr4:79643005..79644726,2	K562	blood:
3	chr4:79641529..79646816-chr4:79652433..79657132,8	K562	blood:

Variant related genes	Relation type
ENSG00000260278	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10008069	0.80[CHB][hapmap]
rs10018189	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs10025599	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs10084949	0.93[ASN][1000 genomes]
rs11724233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11931947	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1275046	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs1275047	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs13101964	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13114489	0.85[ASN][1000 genomes]
rs1346145	0.81[TSI][hapmap]
rs1469289	0.92[ASN][1000 genomes]
rs1469290	0.92[ASN][1000 genomes]
rs1582759	0.91[ASN][1000 genomes]
rs1966537	0.92[ASN][1000 genomes]
rs2288254	0.81[CHD][hapmap]
rs2903578	0.92[ASN][1000 genomes]
rs3822106	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs4246708	0.84[ASN][1000 genomes]
rs4264856	0.80[CHB][hapmap]
rs4365753	0.80[CHB][hapmap]
rs4472162	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4472163	0.80[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs4560439	0.80[CHB][hapmap]
rs6811782	0.96[CEU][hapmap];0.83[MEX][hapmap]
rs6858740	0.96[CEU][hapmap]
rs7672208	0.88[ASN][1000 genomes]
rs7677162	0.88[ASN][1000 genomes]
rs7688534	0.80[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7694971	0.88[ASN][1000 genomes]
rs7699519	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6533951	CXCL10	cis	parietal	SCAN
rs6533951	LIN54	cis	cerebellum	SCAN
rs6533951	ANXA3	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79641000-79644600	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr4:79641200-79644600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr4:79641800-79645600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:79642200-79644400	Enhancers	Liver	Liver
5	chr4:79642400-79644400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:79642400-79644800	Weak transcription	Lung	lung
7	chr4:79642800-79647800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:79642800-79662000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:79643000-79644400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:79643000-79645600	Enhancers	K562	blood
11	chr4:79643200-79644400	Enhancers	Brain Substantia Nigra	brain
12	chr4:79643200-79644600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:79643400-79644400	Weak transcription	Fetal Intestine Large	intestine
14	chr4:79643600-79644400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
15	chr4:79643800-79644400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr4:79643800-79644600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:79643800-79654800	Weak transcription	Right Atrium	heart
18	chr4:79644000-79645000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:79644000-79647200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:79644000-79647800	Weak transcription	GM12878-XiMat	blood
21	chr4:79644000-79647800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr4:79644200-79644400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr4:79644200-79644400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:79644200-79644600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:79644200-79647400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:79644200-79647400	Weak transcription	Primary B cells from cord blood	blood

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