Variant report

Variant	rs3176498
Chromosome Location	chr7:48018707-48018708
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	POLR2A	chr7:48018656-48019486	PFSK-1	brain:	n/a	n/a
2	USF1	chr7:48018557-48019471	H1-hESC	embryonic stem cell:	n/a	chr7:48018811-48018822
3	USF1	chr7:48018493-48019460	H1-hESC	embryonic stem cell:	n/a	chr7:48018811-48018822
4	POLR2A	chr7:48018329-48019508	K562	blood:	n/a	n/a
5	RELA	chr7:48018354-48019454	GM15510	blood:	n/a	n/a
6	E2F6	chr7:48018652-48018867	K562	blood:	n/a	n/a
7	GATA1	chr7:48017746-48019605	PBDE	blood:	n/a	chr7:48018631-48018642
8	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
9	ATF1	chr7:48018348-48019499	K562	blood:	n/a	n/a
10	GABPA	chr7:48018674-48019605	HL-60	blood:	n/a	n/a
11	POLR2A	chr7:48018702-48019498	HL-60	blood:	n/a	n/a
12	SIN3AK20	chr7:48018460-48019435	PANC-1	pancreas:	n/a	n/a
13	GATA3	chr7:48018704-48019615	MCF-7	breast:	n/a	n/a
14	NR2F2	chr7:48018450-48019679	HepG2	liver:	n/a	chr7:48019315-48019330
15	POLR2A	chr7:48018442-48019484	GM12892	blood:	n/a	n/a
16	SMC3	chr7:48018604-48018749	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:48018099-48019561	GM12878	blood:	n/a	n/a
18	EP300	chr7:48018182-48019431	K562	blood:	n/a	n/a
19	EP300	chr7:48018505-48019574	SK-N-SH	brain:	n/a	n/a
20	YY1	chr7:48018631-48019409	GM12878	blood:	n/a	n/a
21	RCOR1	chr7:48018203-48019674	K562	blood:	n/a	n/a
22	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
23	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
24	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
25	POLR2A	chr7:48018588-48019504	NB4	blood:	n/a	n/a
26	RUNX3	chr7:48018571-48019511	GM12878	blood:	n/a	n/a
27	YY1	chr7:48018661-48019484	SK-N-SH	brain:	n/a	n/a
28	ZMIZ1	chr7:48018323-48019780	K562	blood:	n/a	n/a
29	MTA3	chr7:48018267-48019421	GM12878	blood:	n/a	n/a
30	USF1	chr7:48018587-48019306	A549	lung:	n/a	chr7:48018811-48018822
31	ZNF143	chr7:48018209-48019412	K562	blood:	n/a	chr7:48019339-48019357 chr7:48018595-48018604
32	HMGN3	chr7:48018681-48019512	K562	blood:	n/a	n/a
33	MAX	chr7:48018576-48019396	GM12878	blood:	n/a	chr7:48018810-48018818 chr7:48018810-48018823 chr7:48018810-48018823 chr7:48018812-48018821 chr7:48018810-48018823 chr7:48018811-48018822
34	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
35	TBP	chr7:48018662-48019379	HepG2	liver:	n/a	n/a
36	E2F6	chr7:48018554-48019442	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr7:48018530-48019505	HepG2	liver:	n/a	chr7:48018810-48018818 chr7:48018810-48018823 chr7:48018810-48018823 chr7:48018812-48018821 chr7:48018810-48018823 chr7:48018811-48018822
38	MAX	chr7:48018485-48019556	ECC-1	luminal epithelium:	n/a	chr7:48018810-48018818 chr7:48018810-48018823 chr7:48018810-48018823 chr7:48018812-48018821 chr7:48018810-48018823 chr7:48018811-48018822
39	POLR2A	chr7:48018359-48019470	K562	blood:	n/a	n/a
40	USF1	chr7:48018585-48019466	A549	lung:	n/a	chr7:48018811-48018822
41	E2F6	chr7:48018630-48018948	K562	blood:	n/a	n/a
42	POLR2A	chr7:48018101-48019523	PANC-1	pancreas:	n/a	n/a
43	NR2F2	chr7:48018700-48019779	MCF-7	breast:	n/a	chr7:48019315-48019330
44	POLR2A	chr7:48018068-48019450	GM12892	blood:	n/a	n/a
45	ZNF143	chr7:48018676-48019593	H1-hESC	embryonic stem cell:	n/a	chr7:48019339-48019357
46	USF1	chr7:48018489-48019502	SK-N-SH	brain:	n/a	chr7:48018811-48018822
47	E2F6	chr7:48018704-48019391	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr7:48018565-48019335	GM12891	blood:	n/a	n/a
49	RELA	chr7:48018225-48019486	GM18951	blood:	n/a	n/a
50	MXI1	chr7:48018199-48019630	GM12878	blood:	n/a	chr7:48018813-48018822

No.	Distal block	Cell Line	Cell type
1	chr7:48017535..48019169-chr7:48128413..48129998,2	K562	blood:
2	chr7:48016950..48019113-chr7:48039129..48042039,2	K562	blood:
3	chr7:48017568..48020341-chr7:48128356..48131105,2	MCF-7	breast:
4	chr14:77494687..77495502-chr7:48018461..48019313,2	Hela-S3	cervix:
5	chr7:48017456..48020295-chr7:48126750..48129913,5	K562	blood:
6	chr12:32552199..32553014-chr7:48018664..48019299,2	HCT-116	colon:

Variant related genes	Relation type
HUS1	TF binding region
ENSG00000139132	Chromatin interaction
ENSG00000164744	Chromatin interaction
ENSG00000119669	Chromatin interaction
ENSG00000183696	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11973038	0.88[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2307254	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3176499	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176593	1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176602	0.88[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:127 , 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	chr7:48017800-48018800	Flanking Active TSS	Hela-S3	cervix
3	chr7:48018000-48018800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:48018000-48018800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:48018000-48018800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr7:48018000-48018800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:48018000-48018800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr7:48018000-48018800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr7:48018000-48018800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:48018000-48018800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr7:48018000-48018800	Flanking Active TSS	Liver	Liver
12	chr7:48018000-48018800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr7:48018000-48018800	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr7:48018000-48019600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:48018000-48019600	Active TSS	NHDF-Ad	bronchial
16	chr7:48018000-48019800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:48018000-48019800	Active TSS	Fetal Brain Female	brain
18	chr7:48018200-48018800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr7:48018200-48018800	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr7:48018200-48018800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr7:48018200-48018800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr7:48018200-48018800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr7:48018200-48018800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr7:48018200-48018800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:48018200-48018800	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr7:48018200-48018800	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr7:48018200-48018800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr7:48018200-48018800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr7:48018200-48018800	Flanking Active TSS	HUVEC	blood vessel
30	chr7:48018200-48018800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr7:48018200-48018800	Flanking Active TSS	Osteobl	bone
32	chr7:48018200-48019200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:48018200-48019600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:48018200-48019600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:48018200-48019600	Active TSS	Aorta	Aorta
36	chr7:48018200-48019800	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr7:48018200-48020000	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr7:48018400-48018800	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:48018400-48018800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
40	chr7:48018400-48018800	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr7:48018400-48018800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr7:48018400-48018800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:48018400-48018800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:48018400-48018800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr7:48018400-48018800	Flanking Active TSS	NHEK	skin
46	chr7:48018400-48019000	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr7:48018400-48019200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr7:48018400-48019200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:48018400-48019200	Active TSS	Lung	lung
50	chr7:48018400-48019200	Active TSS	Small Intestine	intestine

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