Variant report

Variant	rs6742843
Chromosome Location	chr2:38854024-38854025
allele	C/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	chr2:38853457..38857426-chr2:38859030..38862948,5	K562	blood:
3	chr2:38850061..38855322-chr2:38870938..38874508,5	K562	blood:

Variant related genes	Relation type
ENSG00000235586	Chromatin interaction
ENSG00000143889	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10204680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495880	0.82[CEU][hapmap]
rs12329205	0.83[JPT][hapmap]
rs12991911	0.82[CEU][hapmap]
rs12992482	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13010091	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13011896	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13015860	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13016108	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13016885	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025153	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13032371	0.81[EUR][1000 genomes]
rs13415823	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13431551	0.83[JPT][hapmap]
rs13432435	0.85[EUR][1000 genomes]
rs13432610	0.83[AMR][1000 genomes]
rs17022983	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17022996	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17493573	0.82[CEU][hapmap]
rs17493692	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17575960	0.82[CEU][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2116383	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2217537	0.87[EUR][1000 genomes]
rs2253519	0.83[JPT][hapmap]
rs2373420	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373421	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2373422	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2373423	0.83[JPT][hapmap]
rs34145681	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34450185	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35273515	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35613649	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35861429	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6544169	1.00[JPT][hapmap]
rs6544170	0.84[MEX][hapmap]
rs6721860	1.00[JPT][hapmap]
rs67326552	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6733950	0.94[JPT][hapmap]
rs6745646	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs6749343	0.86[ASN][1000 genomes]
rs6757844	1.00[JPT][hapmap]
rs72909831	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7561778	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7583318	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7600802	0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs919698	0.87[JPT][hapmap];0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6742843	CRIM1	cis	parietal	SCAN

Chromatin state (count:21 , 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	chr2:38849800-38855400	Weak transcription	GM12878-XiMat	blood
3	chr2:38849800-38855600	Enhancers	Fetal Thymus	thymus
4	chr2:38850000-38854800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:38852400-38854400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr2:38853000-38854400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr2:38853000-38854400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:38853000-38854600	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:38853000-38854600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:38853000-38854800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:38853000-38855000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:38853200-38854200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:38853200-38854600	Flanking Active TSS	Dnd41	blood
14	chr2:38853400-38854200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:38853800-38854200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:38853800-38854800	Enhancers	K562	blood
17	chr2:38854000-38854600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr2:38854000-38855000	Flanking Active TSS	HepG2	liver
19	chr2:38854000-38855200	Enhancers	Thymus	Thymus
20	chr2:38854000-38855600	Enhancers	Stomach Mucosa	stomach
21	chr2:38854000-38861200	Weak transcription	Primary T cells from cord blood	blood

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