Variant report

Variant	rs1177578
Chromosome Location	chr12:66524455-66524456
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:416)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:416 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:66524257-66525059	K562	blood:	n/a	n/a
2	POLR2A	chr12:66524284-66524902	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr12:66524330-66524747	A549	lung:	n/a	n/a
4	CHD2	chr12:66524217-66524868	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:66524207-66524866	HUVEC	blood vessel:	n/a	n/a
6	GTF2B	chr12:66524433-66524705	K562	blood:	n/a	n/a
7	CCNT2	chr12:66524430-66524898	K562	blood:	n/a	n/a
8	POLR2A	chr12:66523828-66525082	GM18505	blood:	n/a	n/a
9	ATF2	chr12:66524208-66524815	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr12:66524210-66524633	A549	lung:	n/a	n/a
11	MYC	chr12:66524277-66524834	K562	blood:	n/a	n/a
12	YY1	chr12:66524262-66524912	A549	lung:	n/a	n/a
13	CBX3	chr12:66524292-66524948	K562	blood:	n/a	n/a
14	MAFK	chr12:66524151-66525142	HepG2	liver:	n/a	chr12:66524718-66524729
15	IRF1	chr12:66524113-66524861	K562	blood:	n/a	n/a
16	TBP	chr12:66524293-66524997	K562	blood:	n/a	n/a
17	POLR2A	chr12:66524226-66524880	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:66523966-66525318	GM18526	blood:	n/a	n/a
19	TAF1	chr12:66524288-66524759	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:66523758-66525331	GM12878	blood:	n/a	n/a
21	GABPA	chr12:66524332-66524739	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr12:66524315-66524868	SK-N-SH_RA	brain:	n/a	n/a
23	MAX	chr12:66524048-66524942	Hela-S3	cervix:	n/a	n/a
24	NFIC	chr12:66524147-66524781	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:66523783-66525067	Raji	blood:	n/a	n/a
26	MYC	chr12:66524024-66525587	K562	blood:	n/a	n/a
27	MTA3	chr12:66523668-66525489	GM12878	blood:	n/a	n/a
28	SIN3AK20	chr12:66524218-66524783	HepG2	liver:	n/a	n/a
29	MBD4	chr12:66524286-66524643	HepG2	liver:	n/a	n/a
30	TAF1	chr12:66524235-66524828	PFSK-1	brain:	n/a	n/a
31	RFX5	chr12:66523773-66525271	Hela-S3	cervix:	n/a	n/a
32	YY1	chr12:66524455-66524811	H1-hESC	embryonic stem cell:	n/a	n/a
33	ETS1	chr12:66524203-66524728	A549	lung:	n/a	chr12:66524517-66524533 chr12:66524521-66524530 chr12:66524521-66524530 chr12:66524521-66524530 chr12:66524518-66524531 chr12:66524521-66524530 chr12:66524616-66524625 chr12:66524521-66524530 chr12:66524521-66524530 chr12:66524521-66524530
34	TAF1	chr12:66524000-66524917	A549	lung:	n/a	n/a
35	GABPA	chr12:66524087-66524938	HL-60	blood:	n/a	n/a
36	REST	chr12:66524138-66524972	HL-60	blood:	n/a	chr12:66524631-66524641
37	RUNX3	chr12:66524212-66525038	GM12878	blood:	n/a	n/a
38	CHD1	chr12:66524238-66525026	GM12878	blood:	n/a	n/a
39	MAX	chr12:66524087-66524875	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr12:66524111-66524885	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr12:66523869-66525164	PFSK-1	brain:	n/a	n/a
42	RCOR1	chr12:66524338-66524962	K562	blood:	n/a	n/a
43	YY1	chr12:66524330-66524918	GM12891	blood:	n/a	n/a
44	POLR2A	chr12:66523982-66525010	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr12:66524256-66524801	H1-neurons	neurons:	n/a	n/a
46	BRCA1	chr12:66524260-66524822	GM12878	blood:	n/a	n/a
47	USF1	chr12:66524308-66524774	A549	lung:	n/a	n/a
48	MAX	chr12:66524127-66524990	HepG2	liver:	n/a	n/a
49	SIN3AK20	chr12:66524305-66524816	K562	blood:	n/a	n/a
50	TAF1	chr12:66524095-66525056	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:66524411-66524461	HRCEpiC	kidney:	n/a
2	chr12:66524411-66524461	A549	lung:	n/a
3	chr12:66524411-66524461	K562	blood:	n/a
4	chr12:66524411-66524461	HCT-116	colon:	n/a
5	chr12:66524411-66524461	PANC-1	pancreas:	n/a
6	chr12:66524411-66524461	AG09309	skin:	n/a
7	chr12:66524411-66524461	U87	brain:	n/a
8	chr12:66524411-66524461	T-47D	breast:	n/a
9	chr12:66524411-66524461	AG10803	skin:	n/a
10	chr12:66524411-66524461	HL-60	blood:	n/a
11	chr12:66524411-66524461	GM06990	blood:	n/a
12	chr12:66524411-66524461	AG09319	gingival:	n/a
13	chr12:66524411-66524461	SK-N-MC	brain:	n/a
14	chr12:66524411-66524461	NT2-D1	testis:	n/a
15	chr12:66524411-66524461	HepG2	liver:	n/a
16	chr12:66524411-66524461	HPAEpiC	pulmonary alveolar:	n/a
17	chr12:66524411-66524461	PFSK-1	brain:	n/a
18	chr12:66524411-66524461	GM19239	blood:	n/a
19	chr12:66524411-66524461	BJ	skin:	n/a
20	chr12:66524411-66524461	NH-A	brain:	n/a
21	chr12:66524411-66524461	MCF10A-Er-Src	breast:	n/a
22	chr12:66524411-66524461	MCF-7	breast:	n/a
23	chr12:66524411-66524461	BE2_C	brain:	n/a
24	chr12:66524411-66524461	H1-hESC	embryonic stem cell:	embryo
25	chr12:66524411-66524461	AG04450	lung:	fetal
26	chr12:66524411-66524461	AoSMC	blood vessel:	n/a
27	chr12:66524411-66524461	CMK	blood:	n/a
28	chr12:66524411-66524461	ProgFib	skin:	n/a
29	chr12:66524411-66524461	HRE	kidney:	n/a
30	chr12:66524411-66524461	HMEC	breast:	n/a
31	chr12:66524411-66524461	SK-N-SH	brain:	n/a
32	chr12:66524411-66524461	Jurkat	blood:	n/a
33	chr12:66524411-66524461	HAEpiC	amniotic membrane:	n/a
34	chr12:66524411-66524461	NB4	blood:	n/a
35	chr12:66524411-66524461	GM12878	blood:	n/a
36	chr12:66524411-66524461	HNPCEpiC	eye:	n/a
37	chr12:66524411-66524461	Hela-S3	cervix:	n/a
38	chr12:66524411-66524461	Caco-2	colon:	n/a
39	chr12:66524411-66524461	HCPEpiC	choroid plexus:	n/a
40	chr12:66524411-66524461	GM12892	blood:	n/a
41	chr12:66524411-66524461	ECC-1	luminal epithelium:	n/a
42	chr12:66524411-66524461	RPTEC	kidney:	n/a
43	chr12:66524411-66524461	IMR90	lung:	fetal
44	chr12:66524411-66524461	ovcar-3	ovarian:	n/a
45	chr12:66524411-66524461	NHDF-neo	bronchial:	n/a
46	chr12:66524411-66524461	LNCaP	prostate:	n/a
47	chr12:66524411-66524461	HUVEC	blood vessel:	n/a
48	chr12:66524411-66524461	AG04449	skin:	fetal
49	chr12:66524411-66524461	PrEC	prostate:	n/a
50	chr12:66524411-66524461	HEK293	kidney:	embryo

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66523453..66525027-chr12:66562451..66564555,2	K562	blood:
2	chr12:66523792..66527078-chr12:66561013..66565049,6	MCF-7	breast:
3	chr1:145096186..145098889-chr12:66522673..66525529,2	MCF-7	breast:
4	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
5	chr12:66524431..66524938-chr17:36981117..36982103,2	Hela-S3	cervix:
6	chr12:66523095..66527368-chr12:66532414..66535159,4	MCF-7	breast:
7	chr12:66524156..66526872-chr12:66529144..66534313,4	K562	blood:
8	chr12:66524217..66527472-chr12:66531631..66536698,7	K562	blood:
9	chr12:66523311..66525203-chr12:66696051..66697589,2	MCF-7	breast:
10	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239335	TF binding region
ENSG00000239335	CpG island
ENSG00000263791	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000108296	Chromatin interaction
ENSG00000127311	Chromatin interaction
ENSG00000223380	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10878378	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176057	0.90[CHB][hapmap]
rs11176060	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168735	0.92[EUR][1000 genomes]
rs1168754	0.92[CHB][hapmap]
rs1168765	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168770	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1183892	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs1184556	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1184884	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1185888	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs12823890	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1370126	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1436849	0.83[EUR][1000 genomes]
rs1732886	0.84[CHB][hapmap]
rs1732887	0.90[CHB][hapmap]
rs1732888	0.90[CHB][hapmap]
rs2576187	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701652	0.90[CHB][hapmap]
rs2870782	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4296075	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4328252	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975029	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7979576	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8793	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1177578	TMBIM4	cis	normal skin	skin_eQTL
rs1177578	RP11-745O10.2	cis	Whole Blood	GTEx
rs1177578	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs1177578	RP11-745O10.2	cis	Artery Aorta	GTEx
rs1177578	RP11-745O10.2	cis	Stomach	GTEx
rs1177578	RP11-745O10.2	cis	Esophagus Mucosa	GTEx
rs1177578	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1177578	RP11-745O10.2	cis	Thyroid	GTEx
rs1177578	RP11-745O10.2	cis	Heart Left Ventricle	GTEx
rs1177578	RP11-745O10.2	cis	Artery Tibial	GTEx
rs1177578	TMBIM4	cis	lesional skin	skin_eQTL
rs1177578	TMBIM4	cis	uninvolved skin	skin_eQTL
rs1177578	RP11-745O10.2	cis	lung	GTEx
rs1177578	RP11-745O10.2	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66522600-66526000	Active TSS	GM12878-XiMat	blood
2	chr12:66523000-66525200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:66523000-66525800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:66523000-66526000	Active TSS	A549	lung
5	chr12:66523000-66526400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:66523200-66525200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:66523200-66525400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:66523400-66525000	Active TSS	Fetal Lung	lung
9	chr12:66523400-66525200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr12:66523400-66525200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr12:66523400-66525200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:66523400-66525200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:66523400-66525200	Active TSS	Fetal Intestine Small	intestine
14	chr12:66523400-66525200	Active TSS	NH-A	brain
15	chr12:66523400-66525200	Active TSS	NHDF-Ad	bronchial
16	chr12:66523400-66525400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:66523400-66525400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr12:66523400-66525400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:66523400-66525400	Active TSS	HSMMtube	muscle
20	chr12:66523400-66525400	Active TSS	NHLF	lung
21	chr12:66523400-66525600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:66523400-66525800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr12:66523600-66525000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:66523600-66525000	Active TSS	Gastric	stomach
25	chr12:66523600-66525000	Active TSS	Lung	lung
26	chr12:66523600-66525200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr12:66523600-66525200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:66523600-66525200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr12:66523600-66525200	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr12:66523600-66525400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:66523600-66525400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:66523600-66525400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:66523600-66525400	Active TSS	Fetal Muscle Trunk	muscle
34	chr12:66523600-66525400	Active TSS	Left Ventricle	heart
35	chr12:66523600-66525400	Active TSS	Ovary	ovary
36	chr12:66523600-66525400	Active TSS	Psoas Muscle	Psoas
37	chr12:66523600-66525400	Active TSS	Right Atrium	heart
38	chr12:66523600-66525600	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr12:66523800-66524800	Active TSS	Rectal Smooth Muscle	rectum
40	chr12:66523800-66524800	Active TSS	HUVEC	blood vessel
41	chr12:66523800-66525000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:66523800-66525000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:66523800-66525000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:66523800-66525000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:66523800-66525000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:66523800-66525000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:66523800-66525000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:66523800-66525000	Active TSS	Brain Anterior Caudate	brain
49	chr12:66523800-66525000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr12:66523800-66525000	Active TSS	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links