Variant report

Variant	rs4298438
Chromosome Location	chr7:108258793-108258794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108256349..108259535-chr7:108260988..108264962,5	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1029707	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1029708	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11767037	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11767071	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11773524	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11773875	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17341955	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17426638	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108731	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2215141	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34505662	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55760662	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58954269	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6466244	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67940245	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6945788	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6949766	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6951751	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726608	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs727881	0.81[EUR][1000 genomes]
rs7790890	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7795236	0.83[EUR][1000 genomes]
rs9690171	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs975124	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9768342	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9918599	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised 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	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4298438	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs4298438	NRCAM	cis	cerebellum	SCAN
rs4298438	THAP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108255600-108259800	Weak transcription	Fetal Brain Male	brain
2	chr7:108257800-108270800	Weak transcription	Right Atrium	heart
3	chr7:108258000-108259000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr7:108258000-108259000	Enhancers	Liver	Liver
5	chr7:108258200-108259000	Enhancers	H9 Cell Line	embryonic stem cell
6	chr7:108258200-108259400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr7:108258200-108259600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr7:108258200-108259600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr7:108258200-108261000	Enhancers	Adipose Nuclei	Adipose
10	chr7:108258400-108259000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr7:108258600-108259000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:108258600-108259400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:108258600-108259600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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