Variant report

Variant	rs13014417
Chromosome Location	chr2:178417835-178417836
allele	G/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	EP300	chr2:178417379-178417886	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr2:178417290-178418123	K562	blood:	n/a	n/a
3	MYBL2	chr2:178416980-178418214	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:178416718-178417958	MCF-7	breast:	n/a	n/a
5	POLR2A	chr2:178417234-178418640	U87	brain:	n/a	n/a
6	POU2F2	chr2:178417034-178418058	GM12878	blood:	n/a	n/a
7	ELF1	chr2:178417113-178417898	K562	blood:	n/a	chr2:178417533-178417546 chr2:178417536-178417545
8	POLR2A	chr2:178417081-178418062	HUVEC	blood vessel:	n/a	n/a
9	MAX	chr2:178417341-178418239	H1-hESC	embryonic stem cell:	n/a	chr2:178417521-178417530
10	TAF1	chr2:178417623-178418056	HepG2	liver:	n/a	n/a
11	ELF1	chr2:178416957-178418060	K562	blood:	n/a	chr2:178417533-178417546 chr2:178417536-178417545
12	YY1	chr2:178417267-178418076	GM12892	blood:	n/a	n/a
13	ELK1	chr2:178417349-178417996	K562	blood:	n/a	chr2:178417537-178417546 chr2:178417537-178417546
14	POLR2A	chr2:178417468-178418197	SK-N-MC	brain:	n/a	n/a
15	MAX	chr2:178417361-178418310	A549	lung:	n/a	chr2:178417521-178417530
16	POLR2A	chr2:178417112-178418005	GM12878	blood:	n/a	n/a
17	MBD4	chr2:178417234-178418425	HepG2	liver:	n/a	n/a
18	BCLAF1	chr2:178417166-178418342	GM12878	blood:	n/a	chr2:178417797-178417810 chr2:178417537-178417546 chr2:178417897-178417906 chr2:178417894-178417903
19	NFATC1	chr2:178417335-178418095	GM12878	blood:	n/a	n/a
20	MAZ	chr2:178417399-178418348	GM12878	blood:	n/a	chr2:178417521-178417530
21	RUNX3	chr2:178417168-178418244	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr2:178417290-178417996	K562	blood:	n/a	n/a
23	CREB1	chr2:178417350-178418025	K562	blood:	n/a	n/a
24	RUNX3	chr2:178417192-178418333	GM12878	blood:	n/a	n/a
25	TRIM28	chr2:178417187-178418483	K562	blood:	n/a	n/a
26	JUND	chr2:178417178-178417992	A549	lung:	n/a	n/a
27	POLR2A	chr2:178417264-178417977	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr2:178416414-178418517	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr2:178417021-178418000	Gliobla	brain:	n/a	n/a
30	CBX3	chr2:178416623-178418494	K562	blood:	n/a	n/a
31	RAD21	chr2:178417260-178418135	H1-hESC	embryonic stem cell:	n/a	n/a
32	MYC	chr2:178417640-178417841	HepG2	liver:	n/a	n/a
33	BHLHE40	chr2:178417369-178418271	K562	blood:	n/a	n/a
34	GABPA	chr2:178417359-178417942	K562	blood:	n/a	chr2:178417542-178417549
35	NFIC	chr2:178417288-178417982	HepG2	liver:	n/a	n/a
36	MBD4	chr2:178417304-178418145	HepG2	liver:	n/a	n/a
37	MYC	chr2:178417360-178418607	K562	blood:	n/a	chr2:178417521-178417530
38	IRF1	chr2:178417475-178418141	K562	blood:	n/a	n/a
39	REST	chr2:178417376-178418164	A549	lung:	n/a	n/a
40	WRNIP1	chr2:178417423-178418341	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:178417184-178418050	GM19099	blood:	n/a	n/a
42	MXI1	chr2:178417337-178417975	H1-hESC	embryonic stem cell:	n/a	chr2:178417515-178417530 chr2:178417517-178417532
43	ELF1	chr2:178416952-178418084	HepG2	liver:	n/a	chr2:178417533-178417546 chr2:178417536-178417545
44	YY1	chr2:178417311-178418017	ECC-1	luminal epithelium:	n/a	n/a
45	MAFK	chr2:178417718-178418224	Hela-S3	cervix:	n/a	chr2:178417963-178417977
46	MAX	chr2:178417344-178418518	NB4	blood:	n/a	chr2:178417521-178417530
47	TAF1	chr2:178416836-178418223	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr2:178417367-178418408	HepG2	liver:	n/a	n/a
49	POLR2A	chr2:178416594-178418091	GM12878	blood:	n/a	n/a
50	SIX5	chr2:178417349-178417959	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:178027921..178029669-chr2:178417359..178420313,2	K562	blood:
2	chr2:178075873..178078560-chr2:178417023..178418935,2	K562	blood:
3	chr2:178256384..178258999-chr2:178416044..178418294,3	K562	blood:
4	chr2:178417775..178419456-chr2:178465750..178469072,3	K562	blood:
5	chr2:178415963..178418015-chr2:178480825..178484170,3	K562	blood:
6	chr2:178256384..178259130-chr2:178415368..178419750,5	K562	blood:
7	chr2:178416378..178418708-chr2:178482397..178484777,2	MCF-7	breast:
8	chr2:178075873..178078560-chr2:178415979..178418935,3	K562	blood:

Variant related genes	Relation type
TTC30B	TF binding region
ENSG00000170144	Chromatin interaction
ENSG00000229337	Chromatin interaction
ENSG00000116044	Chromatin interaction
ENSG00000263721	Chromatin interaction
ENSG00000018510	Chromatin interaction
ENSG00000237655	Chromatin interaction
ENSG00000213963	Chromatin interaction
ENSG00000236501	Chromatin interaction
ENSG00000197557	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10171135	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10180514	1.00[JPT][hapmap]
rs10181259	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10184488	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs10190306	1.00[JPT][hapmap]
rs10497497	0.84[CEU][hapmap]
rs10497504	0.84[CEU][hapmap]
rs10497505	1.00[JPT][hapmap]
rs10497506	1.00[JPT][hapmap]
rs10497509	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs10754987	1.00[JPT][hapmap]
rs10754988	1.00[JPT][hapmap]
rs10803911	1.00[JPT][hapmap]
rs10803912	0.84[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs10930788	1.00[JPT][hapmap]
rs10930793	1.00[JPT][hapmap]
rs10930796	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1106075	1.00[CHB][hapmap]
rs11679519	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11694988	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11695035	0.87[EUR][1000 genomes]
rs11887886	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11889272	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11889488	0.85[EUR][1000 genomes]
rs12478545	1.00[JPT][hapmap]
rs12988366	0.92[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs13431091	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13431105	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1345138	0.84[CEU][hapmap]
rs1348851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374438	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1446837	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1446838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1446839	0.84[CEU][hapmap]
rs1530965	1.00[JPT][hapmap]
rs16865187	1.00[JPT][hapmap]
rs16865189	1.00[JPT][hapmap]
rs16865191	1.00[JPT][hapmap]
rs16865322	1.00[JPT][hapmap]
rs16865324	1.00[JPT][hapmap]
rs16865337	1.00[JPT][hapmap]
rs16865343	1.00[CHB][hapmap]
rs16865359	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865376	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865377	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865451	1.00[CHB][hapmap]
rs16865493	1.00[CHB][hapmap]
rs16865498	1.00[CHB][hapmap]
rs16865576	1.00[CHB][hapmap]
rs1838890	0.88[ASN][1000 genomes]
rs1852530	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1867905	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1901823	1.00[JPT][hapmap]
rs2121430	0.84[YRI][hapmap]
rs2167902	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2178017	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs2218575	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2293475	0.84[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs2364851	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2364852	1.00[JPT][hapmap]
rs2365617	0.85[EUR][1000 genomes]
rs2695315	0.84[CEU][hapmap]
rs3754989	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs3813260	1.00[JPT][hapmap]
rs4144278	0.84[CEU][hapmap]
rs4243389	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs4402804	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4585065	1.00[JPT][hapmap]
rs4893829	0.84[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4893940	1.00[JPT][hapmap]
rs4893942	1.00[JPT][hapmap]
rs4893956	0.84[CEU][hapmap]
rs4893970	0.84[CEU][hapmap]
rs6433666	1.00[JPT][hapmap]
rs6433672	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs6433677	1.00[JPT][hapmap]
rs6710109	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs6723014	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6723031	0.84[CEU][hapmap]
rs6723063	0.84[CEU][hapmap]
rs6725331	1.00[JPT][hapmap]
rs6731684	1.00[CHB][hapmap]
rs6732250	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6736145	0.84[EUR][1000 genomes]
rs6737342	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744488	1.00[JPT][hapmap]
rs6748696	1.00[CHB][hapmap]
rs6752528	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756918	0.84[CEU][hapmap]
rs6756948	1.00[CHB][hapmap]
rs7570297	1.00[JPT][hapmap]
rs7582179	0.82[CEU][hapmap]
rs7585952	1.00[JPT][hapmap]
rs7587604	0.84[YRI][hapmap]
rs7588049	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7594073	1.00[JPT][hapmap]
rs7601132	1.00[JPT][hapmap]
rs7604668	1.00[JPT][hapmap]
rs935426	0.84[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13014417	AGPS	cis	cerebellum	SCAN
rs13014417	TTC30B	cis	parietal	SCAN
rs13014417	OSBPL6	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178416200-178418400	Active TSS	Rectal Smooth Muscle	rectum
2	chr2:178416600-178418000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr2:178416600-178418200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:178416600-178418400	Active TSS	Fetal Lung	lung
5	chr2:178416600-178418400	Active TSS	A549	lung
6	chr2:178416600-178418600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:178416600-178418600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:178416600-178418600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:178416600-178418600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr2:178416600-178418600	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr2:178416600-178418600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr2:178416600-178418600	Active TSS	HSMM	muscle
13	chr2:178416800-178418000	Active TSS	Primary T cells from cord blood	blood
14	chr2:178416800-178418000	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr2:178416800-178418200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:178416800-178418200	Active TSS	Thymus	Thymus
17	chr2:178416800-178418400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:178416800-178418400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:178416800-178418400	Active TSS	HSMMtube	muscle
20	chr2:178416800-178418400	Active TSS	NH-A	brain
21	chr2:178416800-178418400	Active TSS	NHLF	lung
22	chr2:178416800-178418600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr2:178416800-178418600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr2:178416800-178418600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:178416800-178418600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:178416800-178418600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr2:178416800-178418600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:178416800-178418600	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr2:178416800-178418600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:178416800-178418600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:178416800-178418600	Active TSS	Fetal Intestine Large	intestine
32	chr2:178416800-178418600	Active TSS	Fetal Intestine Small	intestine
33	chr2:178417000-178418000	Active TSS	GM12878-XiMat	blood
34	chr2:178417000-178418200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:178417000-178418200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:178417000-178418200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:178417000-178418200	Active TSS	Fetal Kidney	kidney
38	chr2:178417000-178418200	Active TSS	Placenta Amnion	Placenta Amnion
39	chr2:178417000-178418200	Active TSS	NHEK	skin
40	chr2:178417000-178418400	Active TSS	H9 Cell Line	embryonic stem cell
41	chr2:178417000-178418400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:178417000-178418400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:178417000-178418400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:178417000-178418400	Active TSS	Aorta	Aorta
45	chr2:178417000-178418400	Active TSS	Brain Angular Gyrus	brain
46	chr2:178417000-178418400	Active TSS	Brain Hippocampus Middle	brain
47	chr2:178417000-178418400	Active TSS	Brain Substantia Nigra	brain
48	chr2:178417000-178418400	Active TSS	Esophagus	oesophagus
49	chr2:178417000-178418400	Active TSS	Fetal Heart	heart
50	chr2:178417000-178418400	Active TSS	Fetal Stomach	stomach

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