Variant report

Variant	rs6544169
Chromosome Location	chr2:38814517-38814518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:38813822-38815492	K562	blood:	n/a	n/a
2	E2F4	chr2:38814231-38814620	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:38813980-38815456	K562	blood:	n/a	n/a
4	IRF1	chr2:38814431-38814867	K562	blood:	n/a	n/a
5	POLR2A	chr2:38813465-38815369	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38808219..38810400-chr2:38813062..38815014,2	MCF-7	breast:
2	chr2:38812622..38815204-chr2:38976239..38979096,3	K562	blood:
3	chr2:38813809..38816046-chr2:38977010..38979745,3	K562	blood:

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10204680	0.94[JPT][hapmap]
rs10495880	0.82[EUR][1000 genomes]
rs12329205	0.81[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap]
rs12987111	0.83[EUR][1000 genomes]
rs12990659	0.83[EUR][1000 genomes]
rs12995222	0.82[EUR][1000 genomes]
rs12996029	0.82[EUR][1000 genomes]
rs13032371	0.83[ASN][1000 genomes]
rs13412171	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs13431551	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13432435	0.90[ASN][1000 genomes]
rs13432610	0.86[ASN][1000 genomes]
rs1368114	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1540436	0.82[EUR][1000 genomes]
rs1579537	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17022996	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17023003	0.93[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs17493573	0.83[EUR][1000 genomes]
rs17575960	0.94[JPT][hapmap]
rs2003209	0.81[ASN][1000 genomes]
rs2099261	0.84[ASN][1000 genomes]
rs2116385	1.00[JPT][hapmap]
rs2163551	0.81[JPT][hapmap]
rs2217537	0.90[ASN][1000 genomes]
rs2253519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2373421	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2373423	0.81[CEU][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs34450185	0.91[ASN][1000 genomes]
rs34462852	0.82[EUR][1000 genomes]
rs35219064	0.81[EUR][1000 genomes]
rs35734673	0.82[EUR][1000 genomes]
rs36057155	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4268910	0.83[EUR][1000 genomes]
rs6721860	0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6733950	0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs6736320	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742843	1.00[JPT][hapmap]
rs6745646	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6749343	0.84[EUR][1000 genomes]
rs6757844	0.81[CEU][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs67772386	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72907903	0.82[EUR][1000 genomes]
rs7571463	0.87[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs7609065	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs919698	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544169	CRIM1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
4	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
5	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
6	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
9	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:38795200-38814800	Weak transcription	Gastric	stomach
12	chr2:38798000-38818000	Weak transcription	Stomach Mucosa	stomach
13	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
14	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:38798600-38816400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:38798800-38817000	Weak transcription	Brain Anterior Caudate	brain
19	chr2:38798800-38822000	Weak transcription	NHEK	skin
20	chr2:38799600-38817200	Weak transcription	Brain Substantia Nigra	brain
21	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:38800000-38817800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:38800000-38818600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:38800600-38816600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:38802800-38819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:38807200-38819000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:38808200-38824400	Weak transcription	Hela-S3	cervix
29	chr2:38808400-38820400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:38808800-38815200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:38808800-38815400	Weak transcription	Ovary	ovary
32	chr2:38808800-38817200	Weak transcription	Placenta	Placenta
33	chr2:38808800-38817800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:38808800-38819000	Strong transcription	Dnd41	blood
35	chr2:38808800-38821800	Weak transcription	HMEC	breast
36	chr2:38808800-38825200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:38808800-38825400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:38808800-38827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:38808800-38827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:38808800-38827400	Weak transcription	Pancreas	Pancrea
41	chr2:38809000-38819600	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:38809000-38824200	Weak transcription	Liver	Liver
43	chr2:38809000-38825600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:38809200-38816000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:38809200-38817600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:38809200-38817800	Weak transcription	Brain Angular Gyrus	brain
47	chr2:38809200-38818000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:38809400-38817200	Weak transcription	HSMMtube	muscle
49	chr2:38809400-38825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:38809600-38827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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