Variant report

Variant	rs3738170
Chromosome Location	chr1:95699604-95699605
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:461)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:461 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr1:95699415-95700159	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr1:95699522-95699795	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr1:95699497-95700124	K562	blood:	n/a	n/a
4	POLR2A	chr1:95699386-95699964	HepG2	liver:	n/a	n/a
5	EP300	chr1:95699555-95699850	T-47D	breast:	n/a	chr1:95699714-95699730
6	GABPA	chr1:95699577-95699898	HepG2	liver:	n/a	n/a
7	NFYA	chr1:95699444-95699779	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr1:95699427-95699935	HepG2	liver:	n/a	n/a
9	ZNF143	chr1:95699498-95699887	K562	blood:	n/a	n/a
10	E2F6	chr1:95699348-95700162	K562	blood:	n/a	chr1:95699734-95699744
11	CREB1	chr1:95699377-95700162	GM12878	blood:	n/a	n/a
12	TBP	chr1:95699104-95700246	K562	blood:	n/a	n/a
13	CTCF	chr1:95699535-95699875	Spleen_OC	spleen:	n/a	n/a
14	RCOR1	chr1:95698181-95700584	IMR90	lung:	n/a	n/a
15	RCOR1	chr1:95699526-95699983	GM12878	blood:	n/a	n/a
16	TAL1	chr1:95699566-95699876	K562	blood:	n/a	n/a
17	TAF1	chr1:95699518-95699964	H1-hESC	embryonic stem cell:	n/a	n/a
18	EGR1	chr1:95699195-95700124	HCT-116	colon:	n/a	chr1:95699730-95699740 chr1:95699651-95699665
19	CTCF	chr1:95699546-95699885	GM19240	blood:	n/a	n/a
20	EGR1	chr1:95699381-95700126	HCT-116	colon:	n/a	chr1:95699730-95699740 chr1:95699651-95699665
21	CTCF	chr1:95699501-95699924	IMR90	lung:	n/a	n/a
22	MAX	chr1:95699310-95700144	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr1:95699292-95700040	A549	lung:	n/a	n/a
24	CTCF	chr1:95699568-95699856	Pancreas_OC	pancreas:	n/a	n/a
25	SP1	chr1:95699284-95699935	A549	lung:	n/a	n/a
26	CBX3	chr1:95699358-95700104	K562	blood:	n/a	n/a
27	PML	chr1:95699381-95700142	GM12878	blood:	n/a	n/a
28	CTCF	chr1:95699600-95699750	AG04449	skin:	n/a	n/a
29	CTCF	chr1:95699502-95699789	A549	lung:	n/a	n/a
30	RAD21	chr1:95699474-95700062	A549	lung:	n/a	n/a
31	POLR2A	chr1:95699574-95699949	A549	lung:	n/a	n/a
32	MAX	chr1:95699500-95699981	HepG2	liver:	n/a	n/a
33	MXI1	chr1:95699542-95699894	Hela-S3	cervix:	n/a	n/a
34	ELK1	chr1:95699574-95699960	GM12878	blood:	n/a	n/a
35	YY1	chr1:95699536-95699920	GM12891	blood:	n/a	chr1:95699733-95699747
36	MAX	chr1:95699323-95700201	ECC-1	luminal epithelium:	n/a	chr1:95700157-95700167
37	POLR2A	chr1:95699563-95700101	GM12878	blood:	n/a	n/a
38	RAD21	chr1:95699489-95699893	K562	blood:	n/a	n/a
39	TCF7L2	chr1:95699419-95699804	PANC-1	pancreas:	n/a	n/a
40	TAF1	chr1:95699512-95699962	HepG2	liver:	n/a	n/a
41	YY1	chr1:95699594-95699990	HepG2	liver:	n/a	chr1:95699733-95699747
42	POLR2A	chr1:95699278-95700285	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr1:95699600-95699750	NHLF	lung:	n/a	n/a
44	POLR2A	chr1:95699345-95699618	U87	brain:	n/a	n/a
45	SIN3AK20	chr1:95699503-95700124	K562	blood:	n/a	n/a
46	MAX	chr1:95699088-95700077	GM12878	blood:	n/a	n/a
47	E2F6	chr1:95699274-95699827	A549	lung:	n/a	chr1:95699734-95699744
48	ELK1	chr1:95699248-95699861	K562	blood:	n/a	n/a
49	POLR2A	chr1:95699479-95699979	K562	blood:	n/a	n/a
50	TCF3	chr1:95699596-95699876	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:95699574-95699624	HIPEpiC	eye:	n/a
2	chr1:95699556-95699606	NH-A	brain:	n/a
3	chr1:95699574-95699624	HPAEpiC	pulmonary alveolar:	n/a
4	chr1:95699556-95699606	HEK293	kidney:	embryo
5	chr1:95699574-95699624	A549	lung:	n/a
6	chr1:95699574-95699624	HMEC	breast:	n/a
7	chr1:95699556-95699606	ovcar-3	ovarian:	n/a
8	chr1:95699574-95699624	GM12878	blood:	n/a
9	chr1:95699574-95699624	AG04450	lung:	fetal
10	chr1:95699574-95699624	SKMC	muscle:	n/a
11	chr1:95699574-95699624	K562	blood:	n/a
12	chr1:95699574-95699624	HEK293	kidney:	embryo
13	chr1:95699556-95699606	CMK	blood:	n/a
14	chr1:95699556-95699606	AG04449	skin:	fetal
15	chr1:95699574-95699624	HRE	kidney:	n/a
16	chr1:95699556-95699606	K562	blood:	n/a
17	chr1:95699574-95699624	ProgFib	skin:	n/a
18	chr1:95699556-95699606	A549	lung:	n/a
19	chr1:95699556-95699606	Hepatocyte	liver:	n/a
20	chr1:95699556-95699606	Hela-S3	cervix:	n/a
21	chr1:95699574-95699624	SK-N-SH_RA	brain:	n/a
22	chr1:95699556-95699606	Caco-2	colon:	n/a
23	chr1:95699574-95699624	HAEpiC	amniotic membrane:	n/a
24	chr1:95699574-95699624	HL-60	blood:	n/a
25	chr1:95699556-95699606	H1-hESC	embryonic stem cell:	embryo
26	chr1:95699574-95699624	RPTEC	kidney:	n/a
27	chr1:95699574-95699624	NH-A	brain:	n/a
28	chr1:95699556-95699606	GM06990	blood:	n/a
29	chr1:95699556-95699606	AG09309	skin:	n/a
30	chr1:95699574-95699624	GM12892	blood:	n/a
31	chr1:95699574-95699624	NB4	blood:	n/a
32	chr1:95699574-95699624	Hela-S3	cervix:	n/a
33	chr1:95699556-95699606	SK-N-SH_RA	brain:	n/a
34	chr1:95699556-95699606	GM12891	blood:	n/a
35	chr1:95699556-95699606	NHDF-neo	bronchial:	n/a
36	chr1:95699556-95699606	HCM	heart:	n/a
37	chr1:95699574-95699624	AG04449	skin:	fetal
38	chr1:95699574-95699624	BE2_C	brain:	n/a
39	chr1:95699556-95699606	IMR90	lung:	fetal
40	chr1:95699556-95699606	HRE	kidney:	n/a
41	chr1:95699574-95699624	CMK	blood:	n/a
42	chr1:95699574-95699624	HCM	heart:	n/a
43	chr1:95699556-95699606	AG10803	skin:	n/a
44	chr1:95699574-95699624	U87	brain:	n/a
45	chr1:95699556-95699606	HepG2	liver:	n/a
46	chr1:95699556-95699606	ProgFib	skin:	n/a
47	chr1:95699556-95699606	PFSK-1	brain:	n/a
48	chr1:95699556-95699606	HCF	heart:	n/a
49	chr1:95699574-95699624	T-47D	breast:	n/a
50	chr1:95699556-95699606	HRPEpiC	eye:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:95581745..95584156-chr1:95699309..95702187,2	MCF-7	breast:
2	chr1:95581571..95584597-chr1:95698513..95700535,3	MCF-7	breast:
3	chr1:95582616..95585939-chr1:95698259..95700506,4	K562	blood:
4	chr1:95536810..95539827-chr1:95698878..95701315,3	K562	blood:
5	chr1:95582496..95583191-chr1:95699224..95700072,2	K562	blood:
6	chr1:95582556..95585358-chr1:95698094..95701319,5	K562	blood:
7	chr1:95537299..95540042-chr1:95699496..95701047,2	K562	blood:

No data

Variant related genes	Relation type
RWDD3	TF binding region
ENSG00000226026	TF binding region
ENSG00000226026	CpG island
RWDD3	CpG island
ENSG00000231992	Chromatin interaction
ENSG00000271092	Chromatin interaction
ENSG00000152078	Chromatin interaction
ENSG00000172339	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10874908	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165343	0.88[ASN][1000 genomes]
rs11165346	0.93[ASN][1000 genomes]
rs11165349	0.94[ASN][1000 genomes]
rs12034397	0.93[ASN][1000 genomes]
rs12037572	0.87[ASN][1000 genomes]
rs12401359	0.94[ASN][1000 genomes]
rs12408858	0.89[ASN][1000 genomes]
rs1927043	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2147587	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296308	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs259340	0.92[ASN][1000 genomes]
rs259341	0.92[ASN][1000 genomes]
rs259348	0.92[ASN][1000 genomes]
rs259351	0.93[ASN][1000 genomes]
rs259353	0.93[ASN][1000 genomes]
rs259356	0.93[ASN][1000 genomes]
rs3738171	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3753872	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767313	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3767315	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820345	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4950024	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs547339	0.94[ASN][1000 genomes]
rs564610	0.92[ASN][1000 genomes]
rs592097	0.93[ASN][1000 genomes]
rs61771764	0.86[ASN][1000 genomes]
rs61771765	0.88[ASN][1000 genomes]
rs61771766	0.88[ASN][1000 genomes]
rs658018	0.93[ASN][1000 genomes]
rs6666528	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671408	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688633	0.92[ASN][1000 genomes]
rs7528790	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 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	chr1:95698200-95700400	Active TSS	Aorta	Aorta
2	chr1:95698200-95700600	Active TSS	Colon Smooth Muscle	Colon
3	chr1:95698200-95700600	Active TSS	Ovary	ovary
4	chr1:95698200-95700600	Active TSS	Right Atrium	heart
5	chr1:95698200-95700600	Active TSS	A549	lung
6	chr1:95698400-95700400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:95698400-95700600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:95698400-95700600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:95698400-95700600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:95698400-95700600	Active TSS	Fetal Kidney	kidney
11	chr1:95698400-95700600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:95698600-95700400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:95698600-95700600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:95698600-95700600	Active TSS	Brain Anterior Caudate	brain
15	chr1:95698600-95700600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:95698600-95700600	Active TSS	Fetal Intestine Large	intestine
17	chr1:95698600-95700600	Active TSS	Right Ventricle	heart
18	chr1:95698600-95700600	Active TSS	NHDF-Ad	bronchial
19	chr1:95698800-95700200	Active TSS	Brain Angular Gyrus	brain
20	chr1:95698800-95700400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:95698800-95700400	Active TSS	Brain Substantia Nigra	brain
22	chr1:95698800-95700400	Active TSS	Colonic Mucosa	Colon
23	chr1:95698800-95700400	Active TSS	Esophagus	oesophagus
24	chr1:95698800-95700400	Active TSS	Gastric	stomach
25	chr1:95698800-95700400	Active TSS	Left Ventricle	heart
26	chr1:95698800-95700400	Active TSS	Placenta Amnion	Placenta Amnion
27	chr1:95698800-95700400	Active TSS	Psoas Muscle	Psoas
28	chr1:95698800-95700600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr1:95698800-95700600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:95698800-95700600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr1:95698800-95700600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr1:95698800-95700600	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:95698800-95700600	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr1:95698800-95700600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:95698800-95700600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:95698800-95700600	Active TSS	Fetal Brain Female	brain
37	chr1:95698800-95700600	Active TSS	Fetal Intestine Small	intestine
38	chr1:95698800-95700600	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:95698800-95700600	Active TSS	HepG2	liver
40	chr1:95699000-95700200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:95699000-95700200	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr1:95699000-95700400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:95699000-95700400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:95699000-95700400	Active TSS	Brain Hippocampus Middle	brain
45	chr1:95699000-95700400	Active TSS	Small Intestine	intestine
46	chr1:95699000-95700400	Active TSS	Spleen	Spleen
47	chr1:95699000-95700600	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr1:95699000-95700600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:95699000-95700600	Active TSS	NHLF	lung
50	chr1:95699000-95700800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links