Variant report

Variant	rs2648734
Chromosome Location	chr5:52068573-52068574
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	chr5:52067360..52069741-chr5:52083124..52085108,2	K562	blood:

Variant related genes	Relation type
ENSG00000248898	Chromatin interaction
ENSG00000213949	Chromatin interaction
ENSG00000152684	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1363958	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1363959	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1363960	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1363961	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16880238	0.93[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs16880266	0.93[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs17209816	1.00[CEU][hapmap]
rs1833883	0.96[ASN][1000 genomes]
rs1833884	0.94[ASN][1000 genomes]
rs193438	0.94[ASN][1000 genomes]
rs2133476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2173525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245991	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245997	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs244484	0.81[ASN][1000 genomes]
rs244485	0.94[ASN][1000 genomes]
rs244488	0.89[ASN][1000 genomes]
rs2548503	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548504	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548505	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548506	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548507	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2648732	0.93[ASN][1000 genomes]
rs2648733	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2648735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2648737	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs3096173	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1027410	chr5:52022713-52103360	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1024123	chr5:52052104-52089545	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020640	chr5:52058830-52120858	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2648734	SH2D2A	trans	brain	seeQTL
rs2648734	TTR	trans	brain	seeQTL
rs2648734	CRX	trans	brain	seeQTL
rs2648734	GUCA1C	trans	brain	seeQTL
rs2648734	LRTM1	trans	brain	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52053200-52069600	Weak transcription	Right Atrium	heart
2	chr5:52066000-52070400	Enhancers	Dnd41	blood
3	chr5:52066800-52072600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:52067000-52070400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr5:52067000-52070800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:52067000-52070800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr5:52067000-52073200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:52067600-52069800	Weak transcription	Fetal Thymus	thymus
9	chr5:52067800-52069800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:52067800-52069800	Weak transcription	Small Intestine	intestine
11	chr5:52068000-52070000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:52068000-52073200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr5:52068200-52068600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:52068400-52068800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:52068400-52069400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:52068400-52071200	Weak transcription	GM12878-XiMat	blood
17	chr5:52068400-52074000	Enhancers	Primary T cells from cord blood	blood

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