Variant report

Variant	rs12257645
Chromosome Location	chr10:49863781-49863782
allele	C/T
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	YY1	chr10:49863533-49863793	A549	lung:	n/a	n/a
2	POLR2A	chr10:49863558-49863824	A549	lung:	n/a	n/a
3	HMGN3	chr10:49863654-49864651	K562	blood:	n/a	chr10:49863685-49863694
4	MAFK	chr10:49863769-49863911	HepG2	liver:	n/a	chr10:49863827-49863838 chr10:49863832-49863847 chr10:49863825-49863839 chr10:49863826-49863837 chr10:49863827-49863838 chr10:49863826-49863837
5	POLR2A	chr10:49863655-49864041	MCF-7	breast:	n/a	n/a
6	RAD21	chr10:49863121-49865128	SK-N-SH	brain:	n/a	chr10:49864471-49864484 chr10:49864454-49864467 chr10:49864406-49864416 chr10:49864470-49864482 chr10:49864472-49864482 chr10:49864108-49864121 chr10:49863692-49863706 chr10:49863461-49863475 chr10:49864468-49864487
7	MAX	chr10:49863388-49864788	A549	lung:	n/a	chr10:49863987-49863997 chr10:49863989-49863996 chr10:49863988-49863997 chr10:49863984-49863999 chr10:49863988-49863997 chr10:49863684-49863693 chr10:49863987-49863998
8	MAFK	chr10:49863679-49863946	IMR90	lung:	n/a	chr10:49863827-49863838 chr10:49863832-49863847 chr10:49863825-49863839 chr10:49863826-49863837 chr10:49863827-49863838 chr10:49863684-49863694 chr10:49863826-49863837
9	MAX	chr10:49863351-49864919	HCT-116	colon:	n/a	chr10:49863987-49863997 chr10:49863989-49863996 chr10:49863988-49863997 chr10:49863984-49863999 chr10:49863988-49863997 chr10:49863684-49863693 chr10:49863987-49863998
10	POLR2A	chr10:49863183-49863916	HUVEC	blood vessel:	n/a	n/a
11	TCF12	chr10:49863547-49864768	ECC-1	luminal epithelium:	n/a	n/a
12	E2F6	chr10:49863461-49864299	A549	lung:	n/a	chr10:49863620-49863630 chr10:49864143-49864153 chr10:49864111-49864121 chr10:49864052-49864061
13	POLR2A	chr10:49863596-49863797	A549	lung:	n/a	n/a
14	CTCF	chr10:49863720-49863870	SK-N-SH_RA	brain:	n/a	n/a
15	TCF12	chr10:49863121-49864869	SK-N-SH	brain:	n/a	n/a
16	JUND	chr10:49863629-49863872	K562	blood:	n/a	chr10:49863684-49863692 chr10:49863684-49863691 chr10:49863683-49863693 chr10:49863682-49863694 chr10:49863684-49863692
17	SMC3	chr10:49863289-49865368	SK-N-SH	brain:	n/a	chr10:49864343-49864353 chr10:49864472-49864482 chr10:49864472-49864486
18	MAX	chr10:49863251-49864876	A549	lung:	n/a	chr10:49863987-49863997 chr10:49863989-49863996 chr10:49863988-49863997 chr10:49863984-49863999 chr10:49863988-49863997 chr10:49863684-49863693 chr10:49863987-49863998
19	ZBTB7A	chr10:49863639-49864584	ECC-1	luminal epithelium:	n/a	chr10:49864471-49864480
20	POLR2A	chr10:49863522-49863811	SK-N-SH	brain:	n/a	n/a
21	FOSL2	chr10:49863331-49863999	SK-N-SH	brain:	n/a	chr10:49863684-49863692 chr10:49863684-49863691 chr10:49863683-49863693 chr10:49863682-49863694 chr10:49863684-49863692
22	NFIC	chr10:49863344-49864794	ECC-1	luminal epithelium:	n/a	n/a
23	STAT3	chr10:49863501-49863800	MCF10A-Er-Src	breast:	n/a	n/a
24	MAX	chr10:49863532-49864707	ECC-1	luminal epithelium:	n/a	chr10:49863987-49863997 chr10:49863989-49863996 chr10:49863988-49863997 chr10:49863984-49863999 chr10:49863988-49863997 chr10:49863684-49863693 chr10:49863987-49863998
25	HA-E2F1	chr10:49863320-49864812	MCF-7	breast:	n/a	chr10:49863620-49863630 chr10:49864143-49864153 chr10:49864111-49864121 chr10:49864052-49864061
26	FOS	chr10:49863085-49863912	HUVEC	blood vessel:	n/a	chr10:49863682-49863693 chr10:49863178-49863188 chr10:49863684-49863692 chr10:49863684-49863691 chr10:49863178-49863188 chr10:49863179-49863187 chr10:49863683-49863693 chr10:49863177-49863189 chr10:49863178-49863188 chr10:49863682-49863694 chr10:49863180-49863191 chr10:49863684-49863692 chr10:49863178-49863188
27	POLR2A	chr10:49862911-49864847	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr10:49863369-49865660	SK-N-SH	brain:	n/a	chr10:49864472-49864485 chr10:49864472-49864485 chr10:49864473-49864483 chr10:49864476-49864485 chr10:49864470-49864488 chr10:49864471-49864487 chr10:49864404-49864422 chr10:49863462-49863475
29	SMARCC1	chr10:49863594-49864567	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr10:49863577-49864958	HCT-116	colon:	n/a	chr10:49864472-49864485 chr10:49864472-49864485 chr10:49864473-49864483 chr10:49864476-49864485 chr10:49864470-49864488 chr10:49864471-49864487 chr10:49864404-49864422
31	MAX	chr10:49863438-49864807	ECC-1	luminal epithelium:	n/a	chr10:49863987-49863997 chr10:49863989-49863996 chr10:49863988-49863997 chr10:49863984-49863999 chr10:49863988-49863997 chr10:49863684-49863693 chr10:49863987-49863998
32	SMC3	chr10:49863493-49864662	Hela-S3	cervix:	n/a	chr10:49864343-49864353 chr10:49864472-49864482 chr10:49864472-49864486
33	CTCF	chr10:49863720-49863870	A549	lung:	n/a	n/a
34	POLR2A	chr10:49863227-49864766	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr10:49863248-49863942	U87	brain:	n/a	n/a
36	POLR2A	chr10:49863116-49864072	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr10:49863211-49863942	U87	brain:	n/a	n/a
38	RCOR1	chr10:49863355-49865134	IMR90	lung:	n/a	n/a
39	NFIC	chr10:49863341-49863964	SK-N-SH	brain:	n/a	n/a
40	NR2F2	chr10:49863323-49865221	MCF-7	breast:	n/a	chr10:49863372-49863387
41	POLR2A	chr10:49863559-49863806	A549	lung:	n/a	n/a
42	SETDB1	chr10:49863555-49864658	K562	blood:	n/a	n/a
43	MAX	chr10:49863568-49864671	K562	blood:	n/a	chr10:49863987-49863997 chr10:49863989-49863996 chr10:49863988-49863997 chr10:49863984-49863999 chr10:49863988-49863997 chr10:49863684-49863693 chr10:49863987-49863998
44	POLR2A	chr10:49863090-49864904	U87	brain:	n/a	n/a
45	E2F6	chr10:49863592-49864161	A549	lung:	n/a	chr10:49863620-49863630 chr10:49864143-49864153 chr10:49864111-49864121 chr10:49864052-49864061
46	E2F4	chr10:49863550-49864644	K562	blood:	n/a	chr10:49863620-49863630 chr10:49864143-49864153 chr10:49864111-49864121 chr10:49864052-49864061
47	MYC	chr10:49863596-49864124	MCF-7	breast:	n/a	chr10:49863987-49863997 chr10:49863984-49863999 chr10:49863989-49863996 chr10:49863988-49863997 chr10:49863988-49863997 chr10:49863684-49863693 chr10:49863987-49863998
48	FOS	chr10:49863520-49863886	MCF10A-Er-Src	breast:	n/a	chr10:49863682-49863693 chr10:49863684-49863692 chr10:49863684-49863691 chr10:49863683-49863693 chr10:49863682-49863694 chr10:49863684-49863692
49	MAX	chr10:49863633-49864779	HepG2	liver:	n/a	chr10:49863987-49863997 chr10:49863989-49863996 chr10:49863988-49863997 chr10:49863984-49863999 chr10:49863988-49863997 chr10:49863684-49863693 chr10:49863987-49863998
50	UBTF	chr10:49863747-49864729	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49714827..49719872-chr10:49861427..49864767,4	K562	blood:

Variant related genes	Relation type
ARHGAP22	TF binding region
ENSG00000248682	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10857616	0.88[ASN][1000 genomes]
rs11101416	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2377595	0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2377596	0.90[ASN][1000 genomes]
rs2377612	0.96[ASN][1000 genomes]
rs2377613	0.96[ASN][1000 genomes]
rs2377614	0.96[ASN][1000 genomes]
rs2377615	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377616	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377618	0.89[EUR][1000 genomes]
rs4240515	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4373841	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375365	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4525142	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4562728	0.81[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs7087882	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7087885	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911516	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12257645	FRMPD2	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49862400-49864600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr10:49862800-49863800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
3	chr10:49863000-49863800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:49863200-49863800	Enhancers	Spleen	Spleen
5	chr10:49863200-49864000	Flanking Active TSS	NH-A	brain
6	chr10:49863200-49864200	Flanking Active TSS	HUVEC	blood vessel
7	chr10:49863200-49864600	Active TSS	Brain Hippocampus Middle	brain
8	chr10:49863200-49864800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr10:49863200-49865000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr10:49863200-49865200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr10:49863400-49863800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:49863400-49863800	Bivalent Enhancer	Primary B cells from cord blood	blood
13	chr10:49863400-49863800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr10:49863400-49863800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr10:49863400-49863800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
16	chr10:49863400-49863800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr10:49863400-49863800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
18	chr10:49863400-49863800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr10:49863400-49864000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:49863400-49864000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:49863400-49864000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr10:49863400-49864000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr10:49863400-49864000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr10:49863400-49864000	Flanking Active TSS	Liver	Liver
25	chr10:49863400-49864000	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr10:49863400-49864000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr10:49863400-49864000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:49863400-49864000	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr10:49863400-49864000	Flanking Active TSS	Hela-S3	cervix
30	chr10:49863400-49864000	Flanking Bivalent TSS/Enh	NHEK	skin
31	chr10:49863400-49864200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:49863400-49864200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:49863400-49864200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr10:49863400-49864200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr10:49863400-49864200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr10:49863400-49864200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr10:49863400-49864200	Flanking Active TSS	Ovary	ovary
38	chr10:49863400-49864200	Flanking Active TSS	Pancreas	Pancrea
39	chr10:49863400-49864200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
40	chr10:49863400-49864200	Active TSS	Right Atrium	heart
41	chr10:49863400-49864200	Flanking Active TSS	Right Ventricle	heart
42	chr10:49863400-49864200	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr10:49863400-49864200	Flanking Active TSS	HMEC	breast
44	chr10:49863400-49864400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr10:49863400-49864400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:49863400-49864400	Flanking Active TSS	Colonic Mucosa	Colon
47	chr10:49863400-49864400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr10:49863400-49864400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr10:49863400-49864600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr10:49863400-49864600	Active TSS	Psoas Muscle	Psoas

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