Variant report

Variant	rs6425028
Chromosome Location	chr1:186345281-186345282
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:289)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:289 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:186343484-186346756	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:186344028-186345292	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:186343925-186345336	Gliobla	brain:	n/a	n/a
4	POLR2A	chr1:186343876-186345459	HepG2	liver:	n/a	n/a
5	REST	chr1:186344144-186345351	K562	blood:	n/a	chr1:186345295-186345309
6	MAX	chr1:186343946-186345349	A549	lung:	n/a	n/a
7	TCF7L2	chr1:186343626-186345385	Hela-S3	cervix:	n/a	chr1:186343834-186343841
8	PML	chr1:186343478-186345433	GM12878	blood:	n/a	n/a
9	CHD1	chr1:186344067-186345779	GM12878	blood:	n/a	chr1:186344825-186344835
10	POU2F2	chr1:186344137-186345332	GM12878	blood:	n/a	n/a
11	ELF1	chr1:186343930-186345409	HCT-116	colon:	n/a	n/a
12	MAZ	chr1:186343570-186345389	K562	blood:	n/a	n/a
13	MYBL2	chr1:186344083-186345287	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:186343537-186345335	NB4	blood:	n/a	n/a
15	TBP	chr1:186343433-186345520	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:186343917-186345373	GM12892	blood:	n/a	n/a
17	JUND	chr1:186343365-186345433	K562	blood:	n/a	chr1:186344583-186344592
18	JUND	chr1:186343749-186345480	H1-hESC	embryonic stem cell:	n/a	chr1:186344583-186344592
19	POLR2A	chr1:186343407-186345626	K562	blood:	n/a	n/a
20	SMC3	chr1:186344108-186345308	Hela-S3	cervix:	n/a	chr1:186344817-186344831
21	E2F4	chr1:186343529-186345366	K562	blood:	n/a	chr1:186344810-186344821 chr1:186344824-186344833 chr1:186344810-186344821
22	GABPA	chr1:186343774-186345649	MCF-7	breast:	n/a	chr1:186344824-186344833
23	POLR2A	chr1:186343447-186345545	K562	blood:	n/a	n/a
24	POLR2A	chr1:186343850-186345360	H1-neurons	neurons:	n/a	n/a
25	MYC	chr1:186343949-186345398	Hela-S3	cervix:	n/a	n/a
26	RCOR1	chr1:186343541-186345452	K562	blood:	n/a	n/a
27	MAX	chr1:186343877-186345439	A549	lung:	n/a	n/a
28	POLR2A	chr1:186343618-186345305	GM12892	blood:	n/a	n/a
29	ELF1	chr1:186344117-186345362	K562	blood:	n/a	n/a
30	POLR2A	chr1:186343483-186345387	Hela-S3	cervix:	n/a	n/a
31	FOS	chr1:186344401-186345460	MCF10A-Er-Src	breast:	n/a	chr1:186344583-186344592
32	ELF1	chr1:186343998-186345320	MCF-7	breast:	n/a	n/a
33	CREB1	chr1:186344117-186345457	K562	blood:	n/a	n/a
34	POLR2A	chr1:186343877-186345442	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:186344017-186345286	SK-N-SH	brain:	n/a	n/a
36	BCLAF1	chr1:186344247-186345362	K562	blood:	n/a	n/a
37	RCOR1	chr1:186343610-186345431	Hela-S3	cervix:	n/a	n/a
38	CREB1	chr1:186344091-186345319	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr1:186344230-186345316	K562	blood:	n/a	chr1:186344815-186344833 chr1:186344818-186344831
40	EBF1	chr1:186344286-186345395	GM12878	blood:	n/a	chr1:186345011-186345022
41	ELF1	chr1:186343594-186345384	MCF-7	breast:	n/a	n/a
42	HDAC2	chr1:186343931-186345293	MCF-7	breast:	n/a	n/a
43	FOXA1	chr1:186345276-186345740	HepG2	liver:	n/a	n/a
44	MYC	chr1:186344482-186345281	MCF-7	breast:	n/a	n/a
45	HEY1	chr1:186344010-186345287	K562	blood:	n/a	n/a
46	PML	chr1:186344158-186345328	GM12878	blood:	n/a	n/a
47	RCOR1	chr1:186343549-186345294	K562	blood:	n/a	n/a
48	POLR2A	chr1:186344095-186345309	HUVEC	blood vessel:	n/a	n/a
49	MAX	chr1:186343956-186345357	H1-hESC	embryonic stem cell:	n/a	n/a
50	MYC	chr1:186343499-186345841	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:186279942..186281845-chr1:186343325..186346234,2	K562	blood:
2	chr1:186344741..186345283-chr3:169490696..169491576,2	Hela-S3	cervix:
3	chr1:186344996..186345598-chr5:94416998..94417779,2	Hela-S3	cervix:
4	chr1:186341227..186346056-chr1:193025925..193030298,4	K562	blood:
5	chr1:186311436..186314433-chr1:186341934..186345376,3	K562	blood:
6	chr1:186345238..186346752-chr1:186365490..186368054,2	MCF-7	breast:
7	chr1:186345038..186345653-chr17:7387578..7388101,2	Hela-S3	cervix:
8	chr1:186344534..186345474-chr7:104652951..104653817,2	Hela-S3	cervix:
9	chr1:186312933..186317180-chr1:186341100..186346147,6	K562	blood:
10	chr1:186344527..186345358-chr14:35873914..35874649,2	Hela-S3	cervix:
11	chr1:68150336..68151321-chr1:186344545..186345537,2	HCT-116	colon:
12	chr1:186344836..186345496-chr10:79793322..79794064,2	Hela-S3	cervix:
13	chr1:186344475..186345462-chr17:71188366..71189310,2	Hela-S3	cervix:
14	chr1:186345106..186345854-chr17:8150945..8151539,2	Hela-S3	cervix:
15	chr1:186344864..186345494-chr2:88315450..88316119,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
TPR	TF binding region
C1orf27	TF binding region
ENSG00000166685	Chromatin interaction
ENSG00000085274	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000116750	Chromatin interaction
ENSG00000116717	Chromatin interaction
ENSG00000116747	Chromatin interaction
ENSG00000047410	Chromatin interaction
ENSG00000138326	Chromatin interaction
ENSG00000238754	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000202025	Chromatin interaction
ENSG00000100906	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000268662	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000157181	Chromatin interaction
ENSG00000175471	Chromatin interaction
ENSG00000178971	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10494583	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs10494584	0.87[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1406294	0.85[ASN][1000 genomes]
rs16825150	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs16825183	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16825185	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16825201	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16825224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16825243	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16825248	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16825279	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16825335	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17491733	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1919199	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1919200	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2272412	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273777	0.85[ASN][1000 genomes]
rs2273778	0.86[ASN][1000 genomes]
rs2297226	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715477	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3119331	1.00[JPT][hapmap]
rs3131554	0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs34585917	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736595	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3736597	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753565	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766702	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766703	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766704	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766705	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766707	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3820181	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820182	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57040195	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425024	0.85[ASN][1000 genomes]
rs6425027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664763	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6667940	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6678193	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6679066	0.81[ASN][1000 genomes]
rs6689129	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7514615	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525634	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7556543	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]

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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv548399	chr1:186295930-186353461	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
4	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6425028	OCLM	cis	parietal	SCAN
rs6425028	OCLM	cis	cerebellum	SCAN
rs6425028	C1orf27	cis	cerebellum	SCAN
rs6425028	CACNA1E	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186342200-186346600	Active TSS	NHLF	lung
2	chr1:186342400-186345800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:186342400-186346000	Active TSS	Fetal Kidney	kidney
4	chr1:186342400-186346400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:186342600-186345800	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:186342600-186345800	Active TSS	NH-A	brain
7	chr1:186342600-186346000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:186342600-186346000	Active TSS	K562	blood
9	chr1:186342600-186346400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:186342600-186346400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:186342800-186345800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:186342800-186346000	Active TSS	Fetal Brain Female	brain
13	chr1:186342800-186346000	Active TSS	Fetal Stomach	stomach
14	chr1:186342800-186346000	Active TSS	HMEC	breast
15	chr1:186342800-186346000	Active TSS	NHDF-Ad	bronchial
16	chr1:186342800-186346200	Active TSS	A549	lung
17	chr1:186342800-186346400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:186342800-186349000	Active TSS	GM12878-XiMat	blood
19	chr1:186343000-186345400	ZNF genes & repeats	Fetal Brain Male	brain
20	chr1:186343000-186345800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:186343000-186345800	Active TSS	Fetal Intestine Large	intestine
22	chr1:186343000-186345800	Active TSS	Fetal Thymus	thymus
23	chr1:186343000-186345800	Active TSS	Hela-S3	cervix
24	chr1:186343000-186346000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr1:186343000-186346000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:186343000-186346000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:186343000-186346000	Active TSS	Fetal Muscle Leg	muscle
28	chr1:186343000-186346000	Active TSS	Psoas Muscle	Psoas
29	chr1:186343000-186346400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:186343200-186345600	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr1:186343200-186345600	Active TSS	Brain Hippocampus Middle	brain
32	chr1:186343200-186345600	Active TSS	Colon Smooth Muscle	Colon
33	chr1:186343200-186345600	Active TSS	Fetal Lung	lung
34	chr1:186343200-186345600	Active TSS	HUVEC	blood vessel
35	chr1:186343200-186345800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:186343200-186345800	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr1:186343200-186345800	Active TSS	Brain Anterior Caudate	brain
38	chr1:186343200-186345800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr1:186343200-186345800	Active TSS	Fetal Heart	heart
40	chr1:186343200-186345800	Active TSS	Fetal Intestine Small	intestine
41	chr1:186343200-186345800	Active TSS	Ovary	ovary
42	chr1:186343200-186345800	Active TSS	Placenta Amnion	Placenta Amnion
43	chr1:186343200-186345800	Active TSS	Thymus	Thymus
44	chr1:186343200-186346000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:186343200-186346000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:186343200-186346000	Active TSS	Right Ventricle	heart
47	chr1:186343200-186346000	Active TSS	HSMM	muscle
48	chr1:186343200-186346000	Active TSS	NHEK	skin
49	chr1:186343200-186346200	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr1:186343200-186346400	Active TSS	ES-I3 Cell Line	embryonic stem cell

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