Variant report

Variant	rs17023003
Chromosome Location	chr2:38853095-38853096
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38827906..38831148-chr2:38849873..38855053,6	K562	blood:
2	chr2:38850061..38855322-chr2:38870938..38874508,5	K562	blood:
3	chr2:38828271..38831581-chr2:38848960..38853344,4	K562	blood:
4	chr2:38852070..38854007-chr2:38978194..38979843,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235586	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12329205	0.81[CHD][hapmap]
rs13412171	0.86[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13421362	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13431551	0.87[CHD][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap]
rs13432435	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13432610	0.82[ASN][1000 genomes]
rs1368114	0.87[CHD][hapmap]
rs17022996	0.86[CEU][hapmap];0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2217537	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2253519	0.87[CHD][hapmap]
rs2373421	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs2373423	0.84[CHD][hapmap]
rs34450185	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs36057155	0.83[ASN][1000 genomes]
rs6544169	0.93[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs6544171	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6717958	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721860	0.87[CHD][hapmap];0.82[MKK][hapmap]
rs6733950	0.81[CHD][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs6735134	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745646	0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs6751018	0.82[EUR][1000 genomes]
rs6757844	0.81[CHD][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap]
rs7562949	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7566698	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7609065	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv528170	chr2:38853095-38854024	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17023003	CRIM1	cis	parietal	SCAN
rs17023003	MAMSTR	trans	parietal	SCAN
rs17023003	FEZ2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38835400-38862400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:38847400-38853400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:38848200-38854000	Weak transcription	Stomach Mucosa	stomach
4	chr2:38849800-38855400	Weak transcription	GM12878-XiMat	blood
5	chr2:38849800-38855600	Enhancers	Fetal Thymus	thymus
6	chr2:38850000-38854800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:38850400-38853400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:38850400-38853400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:38851800-38853200	Enhancers	Dnd41	blood
10	chr2:38851800-38853200	Enhancers	K562	blood
11	chr2:38851800-38853400	Enhancers	Thymus	Thymus
12	chr2:38852200-38853800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:38852400-38853600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:38852400-38854400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr2:38852600-38854000	Enhancers	HepG2	liver
16	chr2:38853000-38853400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr2:38853000-38854000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr2:38853000-38854000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:38853000-38854400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr2:38853000-38854400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:38853000-38854600	Enhancers	Primary hematopoietic stem cells	blood
22	chr2:38853000-38854600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:38853000-38854800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:38853000-38855000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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