Variant report

Variant	rs3176492
Chromosome Location	chr7:48019415-48019416
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	POLR2A	chr7:48018656-48019486	PFSK-1	brain:	n/a	n/a
2	CREB1	chr7:48018760-48019557	GM12878	blood:	n/a	n/a
3	ZEB1	chr7:48018878-48019486	GM12878	blood:	n/a	n/a
4	BCL3	chr7:48018897-48019431	A549	lung:	n/a	n/a
5	USF1	chr7:48018557-48019471	H1-hESC	embryonic stem cell:	n/a	chr7:48018811-48018822
6	ZNF143	chr7:48018972-48019430	GM12878	blood:	n/a	chr7:48019339-48019357
7	USF1	chr7:48018493-48019460	H1-hESC	embryonic stem cell:	n/a	chr7:48018811-48018822
8	POLR2A	chr7:48018329-48019508	K562	blood:	n/a	n/a
9	RELA	chr7:48018354-48019454	GM15510	blood:	n/a	n/a
10	FOXA2	chr7:48018854-48019471	A549	lung:	n/a	n/a
11	CCNT2	chr7:48018724-48019475	K562	blood:	n/a	n/a
12	CHD1	chr7:48018982-48019511	H1-hESC	embryonic stem cell:	n/a	chr7:48019343-48019353
13	GATA1	chr7:48017746-48019605	PBDE	blood:	n/a	chr7:48018631-48018642
14	MAZ	chr7:48018653-48019512	Hela-S3	cervix:	n/a	chr7:48018810-48018818 chr7:48018810-48018823 chr7:48018810-48018823 chr7:48018812-48018821 chr7:48018810-48018823 chr7:48018811-48018822
15	ATF1	chr7:48018348-48019499	K562	blood:	n/a	n/a
16	GABPA	chr7:48018674-48019605	HL-60	blood:	n/a	n/a
17	SP1	chr7:48018731-48019550	A549	lung:	n/a	chr7:48019273-48019284 chr7:48019343-48019357 chr7:48019270-48019284 chr7:48019261-48019271
18	HNF4A	chr7:48019056-48019488	HepG2	liver:	n/a	chr7:48019323-48019338 chr7:48019318-48019330 chr7:48019324-48019338 chr7:48019319-48019331 chr7:48019310-48019323 chr7:48019324-48019337 chr7:48019318-48019330 chr7:48019317-48019331 chr7:48019320-48019342 chr7:48019310-48019324 chr7:48019311-48019323
19	POLR2A	chr7:48018702-48019498	HL-60	blood:	n/a	n/a
20	SIN3AK20	chr7:48018460-48019435	PANC-1	pancreas:	n/a	n/a
21	GATA3	chr7:48018704-48019615	MCF-7	breast:	n/a	n/a
22	NR2F2	chr7:48018450-48019679	HepG2	liver:	n/a	chr7:48019315-48019330
23	POLR2A	chr7:48018442-48019484	GM12892	blood:	n/a	n/a
24	JUND	chr7:48019039-48019431	HepG2	liver:	n/a	n/a
25	POLR2A	chr7:48018099-48019561	GM12878	blood:	n/a	n/a
26	EP300	chr7:48018182-48019431	K562	blood:	n/a	n/a
27	EP300	chr7:48018505-48019574	SK-N-SH	brain:	n/a	n/a
28	RCOR1	chr7:48018203-48019674	K562	blood:	n/a	n/a
29	ELF1	chr7:48018914-48019524	SK-N-SH	brain:	n/a	chr7:48019382-48019391 chr7:48019218-48019230
30	POLR2A	chr7:48018909-48019415	HepG2	liver:	n/a	n/a
31	MYC	chr7:48018531-48019541	H1-hESC	embryonic stem cell:	n/a	chr7:48018810-48018818 chr7:48018810-48018823 chr7:48018810-48018823 chr7:48018812-48018821 chr7:48018810-48018823 chr7:48018811-48018822
32	MAX	chr7:48018577-48019514	A549	lung:	n/a	chr7:48018810-48018818 chr7:48018810-48018823 chr7:48018810-48018823 chr7:48018812-48018821 chr7:48018810-48018823 chr7:48018811-48018822
33	ZBTB7A	chr7:48019105-48019453	HepG2	liver:	n/a	n/a
34	MYC	chr7:48018159-48019483	K562	blood:	n/a	chr7:48018810-48018818 chr7:48018810-48018823 chr7:48018810-48018823 chr7:48018812-48018821 chr7:48018810-48018823 chr7:48018811-48018822
35	E2F6	chr7:48018876-48019475	A549	lung:	n/a	n/a
36	POLR2A	chr7:48018588-48019504	NB4	blood:	n/a	n/a
37	RUNX3	chr7:48018571-48019511	GM12878	blood:	n/a	n/a
38	NFIC	chr7:48018761-48019476	GM12878	blood:	n/a	n/a
39	RXRA	chr7:48018985-48019454	HepG2	liver:	n/a	chr7:48019305-48019321 chr7:48019288-48019301 chr7:48019289-48019300 chr7:48019309-48019325 chr7:48019323-48019339 chr7:48019314-48019334 chr7:48019310-48019323 chr7:48019321-48019341 chr7:48019332-48019343 chr7:48019317-48019330 chr7:48019310-48019323 chr7:48019317-48019330 chr7:48019307-48019327 chr7:48019310-48019323 chr7:48019317-48019330
40	POLR2A	chr7:48018715-48019470	U87	brain:	n/a	n/a
41	YY1	chr7:48018661-48019484	SK-N-SH	brain:	n/a	n/a
42	NANOG	chr7:48018952-48019452	H1-hESC	embryonic stem cell:	n/a	n/a
43	ZMIZ1	chr7:48018323-48019780	K562	blood:	n/a	n/a
44	MTA3	chr7:48018267-48019421	GM12878	blood:	n/a	n/a
45	SRF	chr7:48018750-48019482	ECC-1	luminal epithelium:	n/a	n/a
46	MEF2A	chr7:48018863-48019467	GM12878	blood:	n/a	n/a
47	HMGN3	chr7:48018681-48019512	K562	blood:	n/a	n/a
48	MAX	chr7:48018539-48019570	HepG2	liver:	n/a	chr7:48018810-48018818 chr7:48018810-48018823 chr7:48018810-48018823 chr7:48018812-48018821 chr7:48018810-48018823 chr7:48018811-48018822
49	E2F6	chr7:48018554-48019442	H1-hESC	embryonic stem cell:	n/a	n/a
50	SP1	chr7:48018777-48019545	A549	lung:	n/a	chr7:48019273-48019284 chr7:48019343-48019357 chr7:48019270-48019284 chr7:48019261-48019271

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:48019388-48019438	SK-N-MC	brain:	n/a
2	chr7:48019388-48019438	GM19239	blood:	n/a
3	chr7:48019388-48019438	HCM	heart:	n/a
4	chr7:48019388-48019438	HEEpiC	esophagus:	n/a
5	chr7:48019388-48019438	HepG2	liver:	n/a
6	chr7:48019388-48019438	PANC-1	pancreas:	n/a
7	chr7:48019388-48019438	SK-N-SH_RA	brain:	n/a
8	chr7:48019388-48019438	ECC-1	luminal epithelium:	n/a
9	chr7:48019388-48019438	GM06990	blood:	n/a
10	chr7:48019388-48019438	HEK293	kidney:	embryo
11	chr7:48019388-48019438	Hela-S3	cervix:	n/a
12	chr7:48019388-48019438	GM12891	blood:	n/a
13	chr7:48019388-48019438	AG09309	skin:	n/a
14	chr7:48019388-48019438	NT2-D1	testis:	n/a
15	chr7:48019388-48019438	A549	lung:	n/a
16	chr7:48019388-48019438	H1-hESC	embryonic stem cell:	embryo
17	chr7:48019388-48019438	MCF10A-Er-Src	breast:	n/a
18	chr7:48019388-48019438	HRPEpiC	eye:	n/a
19	chr7:48019388-48019438	HCT-116	colon:	n/a
20	chr7:48019388-48019438	RPTEC	kidney:	n/a
21	chr7:48019388-48019438	Caco-2	colon:	n/a
22	chr7:48019388-48019438	GM12878	blood:	n/a
23	chr7:48019388-48019438	Jurkat	blood:	n/a
24	chr7:48019388-48019438	NHDF-neo	bronchial:	n/a
25	chr7:48019388-48019438	HNPCEpiC	eye:	n/a
26	chr7:48019388-48019438	HUVEC	blood vessel:	n/a
27	chr7:48019388-48019438	AG04450	lung:	fetal
28	chr7:48019388-48019438	SK-N-SH	brain:	n/a
29	chr7:48019388-48019438	LNCaP	prostate:	n/a
30	chr7:48019388-48019438	NB4	blood:	n/a
31	chr7:48019388-48019438	Hepatocyte	liver:	n/a
32	chr7:48019388-48019438	AoSMC	blood vessel:	n/a
33	chr7:48019388-48019438	HAEpiC	amniotic membrane:	n/a
34	chr7:48019388-48019438	SKMC	muscle:	n/a
35	chr7:48019388-48019438	HRCEpiC	kidney:	n/a
36	chr7:48019388-48019438	HCF	heart:	n/a
37	chr7:48019388-48019438	NHBE	bronchial:	n/a
38	chr7:48019388-48019438	SAEC	small airway:	n/a
39	chr7:48019388-48019438	ProgFib	skin:	n/a
40	chr7:48019388-48019438	HPAEpiC	pulmonary alveolar:	n/a
41	chr7:48019388-48019438	AG10803	skin:	n/a
42	chr7:48019388-48019438	HRE	kidney:	n/a
43	chr7:48019388-48019438	NH-A	brain:	n/a
44	chr7:48019388-48019438	T-47D	breast:	n/a
45	chr7:48019388-48019438	HCPEpiC	choroid plexus:	n/a
46	chr7:48019388-48019438	PFSK-1	brain:	n/a
47	chr7:48019388-48019438	HL-60	blood:	n/a
48	chr7:48019388-48019438	IMR90	lung:	fetal
49	chr7:48019388-48019438	AG04449	skin:	fetal
50	chr7:48019388-48019438	HMEC	breast:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48017568..48020341-chr7:48128356..48131105,2	MCF-7	breast:
2	chr7:48017456..48020295-chr7:48126750..48129913,5	K562	blood:

Variant related genes	Relation type
HUS1	TF binding region
HUS1	CpG island
ENSG00000183696	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11971829	1.00[YRI][hapmap]
rs11973024	1.00[YRI][hapmap]
rs12668946	1.00[YRI][hapmap]
rs12673502	1.00[YRI][hapmap]
rs17710633	1.00[YRI][hapmap]
rs2123609	1.00[YRI][hapmap]
rs3176509	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3176542	1.00[YRI][hapmap]
rs3176543	1.00[YRI][hapmap]
rs3176544	1.00[YRI][hapmap]
rs3176606	1.00[YRI][hapmap]
rs9639988	1.00[YRI][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48017600-48019600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:48018000-48019600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:48018000-48019600	Active TSS	NHDF-Ad	bronchial
4	chr7:48018000-48019800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:48018000-48019800	Active TSS	Fetal Brain Female	brain
6	chr7:48018200-48019600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:48018200-48019600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:48018200-48019600	Active TSS	Aorta	Aorta
9	chr7:48018200-48019800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr7:48018200-48020000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr7:48018400-48019600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr7:48018400-48019600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:48018400-48019600	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr7:48018400-48019600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:48018400-48019600	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr7:48018400-48019600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:48018400-48019600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:48018400-48019600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:48018400-48019600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:48018400-48019600	Active TSS	Fetal Intestine Small	intestine
21	chr7:48018400-48019600	Active TSS	Fetal Muscle Trunk	muscle
22	chr7:48018400-48019600	Active TSS	Left Ventricle	heart
23	chr7:48018400-48019600	Active TSS	Ovary	ovary
24	chr7:48018400-48019600	Active TSS	Pancreas	Pancrea
25	chr7:48018400-48019600	Active TSS	Psoas Muscle	Psoas
26	chr7:48018400-48019600	Active TSS	Right Atrium	heart
27	chr7:48018400-48019600	Active TSS	Right Ventricle	heart
28	chr7:48018400-48019600	Active TSS	GM12878-XiMat	blood
29	chr7:48018400-48019600	Active TSS	HSMM	muscle
30	chr7:48018400-48019600	Active TSS	HSMMtube	muscle
31	chr7:48018400-48019800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr7:48018400-48019800	Active TSS	H9 Cell Line	embryonic stem cell
33	chr7:48018400-48019800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:48018400-48019800	Active TSS	Brain Angular Gyrus	brain
35	chr7:48018400-48019800	Active TSS	Brain Cingulate Gyrus	brain
36	chr7:48018400-48019800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:48018400-48019800	Active TSS	Fetal Brain Male	brain
38	chr7:48018600-48019600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:48018600-48019600	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr7:48018600-48019600	Active TSS	Brain Germinal Matrix	brain
41	chr7:48018600-48019600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr7:48018600-48019600	Active TSS	Brain Substantia Nigra	brain
43	chr7:48018600-48019600	Active TSS	Colonic Mucosa	Colon
44	chr7:48018600-48019600	Active TSS	Colon Smooth Muscle	Colon
45	chr7:48018600-48019600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr7:48018600-48019600	Active TSS	Fetal Intestine Large	intestine
47	chr7:48018600-48019600	Active TSS	Fetal Kidney	kidney
48	chr7:48018600-48019600	Active TSS	Fetal Muscle Leg	muscle
49	chr7:48018600-48019600	Active TSS	Placenta	Placenta
50	chr7:48018600-48019600	Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links