Variant report

Variant	rs6757844
Chromosome Location	chr2:38832850-38832851
allele	C/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	NR3C1	chr2:38832575-38832936	ECC-1	luminal epithelium:	n/a	chr2:38832668-38832677
2	TEAD4	chr2:38832500-38832964	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
2	chr2:38832813..38836255-chr2:38838239..38840067,3	MCF-7	breast:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
5	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000232518	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143891	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10204680	0.94[JPT][hapmap]
rs12329205	0.81[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap]
rs13032371	0.84[ASN][1000 genomes]
rs13393767	0.87[ASN][1000 genomes]
rs13431551	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13432435	0.87[ASN][1000 genomes]
rs13432610	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1368114	0.81[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap]
rs1579537	0.81[CEU][hapmap]
rs17022996	1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs17023003	0.81[CHD][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap]
rs17493538	0.82[EUR][1000 genomes]
rs17493594	0.81[EUR][1000 genomes]
rs17575960	0.94[JPT][hapmap]
rs1864828	0.85[EUR][1000 genomes]
rs2003209	0.82[ASN][1000 genomes]
rs2099261	0.85[ASN][1000 genomes]
rs2116385	1.00[JPT][hapmap]
rs2163551	0.81[JPT][hapmap]
rs2217537	0.87[ASN][1000 genomes]
rs2253519	0.81[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs2373421	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2373423	0.89[ASW][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs34450185	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs36057155	0.87[ASN][1000 genomes]
rs56217714	0.84[EUR][1000 genomes]
rs6544169	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]
rs6544170	0.82[EUR][1000 genomes]
rs6721860	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6733950	0.81[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6742843	1.00[JPT][hapmap]
rs6745023	0.84[EUR][1000 genomes]
rs6745646	0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs67772386	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7571463	0.95[CEU][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7573095	0.81[EUR][1000 genomes]
rs7584547	0.81[CEU][hapmap]
rs7609065	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs891706	0.91[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
rs6757844	CRIM1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38830800-38833800	Weak transcription	HSMM	muscle
2	chr2:38830800-38838600	Weak transcription	Stomach Mucosa	stomach
3	chr2:38831000-38834400	Weak transcription	HSMMtube	muscle
4	chr2:38831000-38834600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:38831000-38834800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:38831000-38834800	Weak transcription	NHLF	lung
7	chr2:38831000-38835000	Weak transcription	NHEK	skin
8	chr2:38831200-38834400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:38831200-38834600	Weak transcription	NH-A	brain
10	chr2:38831200-38834800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:38831200-38834800	Weak transcription	Osteobl	bone
12	chr2:38831200-38840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:38831200-38840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:38831400-38833000	Enhancers	K562	blood
15	chr2:38831400-38834000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:38831400-38834400	Weak transcription	HMEC	breast
17	chr2:38831400-38834600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:38831400-38834600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:38831400-38834600	Weak transcription	A549	lung
20	chr2:38831400-38834800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:38831400-38834800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:38831400-38834800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:38831400-38834800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:38831400-38834800	Weak transcription	Fetal Intestine Large	intestine
25	chr2:38831400-38834800	Weak transcription	Thymus	Thymus
26	chr2:38831400-38835000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:38831400-38835400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:38831400-38836000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:38831400-38836800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:38831400-38838600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:38831400-38838800	Weak transcription	Lung	lung
32	chr2:38831400-38840000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:38831400-38840800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:38831600-38834600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:38831600-38834800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:38831800-38834400	Weak transcription	Dnd41	blood
37	chr2:38832000-38833000	Enhancers	Brain Hippocampus Middle	brain
38	chr2:38832000-38834800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr2:38832000-38834800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:38832200-38835000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr2:38832400-38833000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:38832400-38833600	Enhancers	Fetal Thymus	thymus
43	chr2:38832400-38834400	Enhancers	GM12878-XiMat	blood
44	chr2:38832600-38833000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:38832600-38833200	Enhancers	Fetal Kidney	kidney
46	chr2:38832600-38834600	Weak transcription	HepG2	liver
47	chr2:38832800-38833000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:38832800-38834600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:38832800-38839400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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