Variant report

Variant	rs61787828
Chromosome Location	chr1:98386955-98386956
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:177)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:177 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr1:98386282-98387126	SK-N-SH_RA	brain:	n/a	chr1:98386681-98386692 chr1:98386356-98386365 chr1:98386290-98386301 chr1:98386354-98386365 chr1:98386344-98386358
2	MAX	chr1:98385877-98387202	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr1:98385759-98387405	IMR90	lung:	n/a	n/a
4	MAX	chr1:98385962-98387219	A549	lung:	n/a	n/a
5	ELK1	chr1:98386810-98387176	GM12878	blood:	n/a	n/a
6	E2F4	chr1:98386412-98387082	MCF10A-Er-Src	breast:	n/a	chr1:98386713-98386728
7	POLR2A	chr1:98385244-98387319	MCF10A-Er-Src	breast:	n/a	n/a
8	SIN3AK20	chr1:98385880-98387200	SK-N-SH	brain:	n/a	n/a
9	YY1	chr1:98386632-98387083	H1-hESC	embryonic stem cell:	n/a	chr1:98386681-98386692
10	POLR2A	chr1:98386939-98387162	GM12878	blood:	n/a	n/a
11	BRCA1	chr1:98385801-98387193	Hela-S3	cervix:	n/a	n/a
12	MAZ	chr1:98385123-98387389	IMR90	lung:	n/a	chr1:98387376-98387386
13	TCF7L2	chr1:98385987-98387224	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:98385854-98387130	HUVEC	blood vessel:	n/a	n/a
15	JUND	chr1:98386840-98387152	K562	blood:	n/a	n/a
16	POLR2A	chr1:98385929-98387224	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:98386325-98387030	HUVEC	blood vessel:	n/a	n/a
18	PML	chr1:98386027-98387317	GM12878	blood:	n/a	n/a
19	ELF1	chr1:98386921-98387205	HepG2	liver:	n/a	chr1:98387121-98387134
20	POLR2A	chr1:98386951-98387033	GM12878	blood:	n/a	n/a
21	RUNX3	chr1:98385994-98387308	GM12878	blood:	n/a	n/a
22	MXI1	chr1:98385863-98387170	Hela-S3	cervix:	n/a	n/a
23	STAT1	chr1:98385837-98387150	GM12878	blood:	n/a	chr1:98387077-98387089
24	SIN3A	chr1:98385888-98387289	H1-hESC	embryonic stem cell:	n/a	chr1:98386298-98386311
25	ZKSCAN1	chr1:98386210-98387129	Hela-S3	cervix:	n/a	n/a
26	MXI1	chr1:98386039-98387055	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:98386328-98387128	HepG2	liver:	n/a	n/a
28	ELF1	chr1:98386844-98387189	A549	lung:	n/a	chr1:98387121-98387134
29	ELF1	chr1:98386919-98387228	GM12878	blood:	n/a	chr1:98387121-98387134
30	ZEB1	chr1:98386445-98386961	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:98386242-98387289	U87	brain:	n/a	n/a
32	RAD21	chr1:98385911-98387176	SK-N-SH_RA	brain:	n/a	n/a
33	REST	chr1:98386115-98387309	H1-neurons	neurons:	n/a	chr1:98386344-98386354 chr1:98386676-98386689 chr1:98386298-98386311
34	CTBP2	chr1:98386118-98387330	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:98386024-98387202	Gliobla	brain:	n/a	n/a
36	RCOR1	chr1:98386815-98387140	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:98386136-98387291	U87	brain:	n/a	n/a
38	CTCF	chr1:98386840-98386990	RPTEC	kidney:	n/a	n/a
39	STAT5A	chr1:98386650-98387080	GM12878	blood:	n/a	n/a
40	USF2	chr1:98386898-98387241	Hela-S3	cervix:	n/a	n/a
41	SPI1	chr1:98386844-98387247	GM12878	blood:	n/a	n/a
42	PRDM1	chr1:98386752-98386975	Hela-S3	cervix:	n/a	chr1:98386883-98386898 chr1:98386878-98386892
43	RUNX3	chr1:98385915-98387256	GM12878	blood:	n/a	n/a
44	MXI1	chr1:98386073-98387147	H1-hESC	embryonic stem cell:	n/a	n/a
45	ELF1	chr1:98386335-98387303	GM12878	blood:	n/a	chr1:98386351-98386363 chr1:98387121-98387134
46	POLR2A	chr1:98386179-98387190	GM12878	blood:	n/a	n/a
47	EGR1	chr1:98386299-98387243	H1-hESC	embryonic stem cell:	n/a	chr1:98387125-98387134 chr1:98386815-98386825 chr1:98386353-98386363 chr1:98387008-98387018
48	WRNIP1	chr1:98386585-98387182	GM12878	blood:	n/a	n/a
49	ELK1	chr1:98386460-98387135	Hela-S3	cervix:	n/a	n/a
50	TCF7L2	chr1:98386327-98387156	HCT-116	colon:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:98386915-98386965	LNCaP	prostate:	n/a
2	chr1:98386913-98386963	GM19239	blood:	n/a
3	chr1:98386915-98386965	BJ	skin:	n/a
4	chr1:98386913-98386963	NHDF-neo	bronchial:	n/a
5	chr1:98386913-98386963	AG10803	skin:	n/a
6	chr1:98386913-98386963	HCT-116	colon:	n/a
7	chr1:98386913-98386963	A549	lung:	n/a
8	chr1:98386913-98386963	PFSK-1	brain:	n/a
9	chr1:98386913-98386963	T-47D	breast:	n/a
10	chr1:98386913-98386963	HNPCEpiC	eye:	n/a
11	chr1:98386913-98386963	HEEpiC	esophagus:	n/a
12	chr1:98386915-98386965	A549	lung:	n/a
13	chr1:98386913-98386963	CMK	blood:	n/a
14	chr1:98386913-98386963	HMEC	breast:	n/a
15	chr1:98386913-98386963	BJ	skin:	n/a
16	chr1:98386915-98386965	HRE	kidney:	n/a
17	chr1:98386915-98386965	Hela-S3	cervix:	n/a
18	chr1:98386915-98386965	NT2-D1	testis:	n/a
19	chr1:98386913-98386963	LNCaP	prostate:	n/a
20	chr1:98386913-98386963	Hepatocyte	liver:	n/a
21	chr1:98386913-98386963	MCF10A-Er-Src	breast:	n/a
22	chr1:98386915-98386965	IMR90	lung:	fetal
23	chr1:98386915-98386965	Caco-2	colon:	n/a
24	chr1:98386915-98386965	HCT-116	colon:	n/a
25	chr1:98386913-98386963	NHBE	bronchial:	n/a
26	chr1:98386915-98386965	SK-N-MC	brain:	n/a
27	chr1:98386915-98386965	Hepatocyte	liver:	n/a
28	chr1:98386915-98386965	NHBE	bronchial:	n/a
29	chr1:98386913-98386963	SKMC	muscle:	n/a
30	chr1:98386913-98386963	NT2-D1	testis:	n/a
31	chr1:98386913-98386963	ProgFib	skin:	n/a
32	chr1:98386915-98386965	GM12878	blood:	n/a
33	chr1:98386913-98386963	HL-60	blood:	n/a
34	chr1:98386913-98386963	MCF-7	breast:	n/a
35	chr1:98386915-98386965	HEK293	kidney:	embryo
36	chr1:98386915-98386965	HRCEpiC	kidney:	n/a
37	chr1:98386915-98386965	AG04449	skin:	fetal
38	chr1:98386915-98386965	AG10803	skin:	n/a
39	chr1:98386913-98386963	HCM	heart:	n/a
40	chr1:98386915-98386965	K562	blood:	n/a
41	chr1:98386913-98386963	NH-A	brain:	n/a
42	chr1:98386915-98386965	HAEpiC	amniotic membrane:	n/a
43	chr1:98386915-98386965	HCM	heart:	n/a
44	chr1:98386915-98386965	HIPEpiC	eye:	n/a
45	chr1:98386915-98386965	SKMC	muscle:	n/a
46	chr1:98386913-98386963	HPAEpiC	pulmonary alveolar:	n/a
47	chr1:98386913-98386963	HAEpiC	amniotic membrane:	n/a
48	chr1:98386913-98386963	HCPEpiC	choroid plexus:	n/a
49	chr1:98386913-98386963	AG09309	skin:	n/a
50	chr1:98386913-98386963	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type
1	chr1:98386321..98387273-chr3:197518075..197518651,2	Hela-S3	cervix:
2	chr1:98386869..98389236-chr1:98393890..98395524,2	MCF-7	breast:
3	chr1:98386898..98389575-chr1:98395488..98397277,2	K562	blood:

No data

Variant related genes	Relation type
DPYD	TF binding region
DPYD	CpG island
ENSG00000186001	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10875118	0.82[ASN][1000 genomes]
rs10875120	0.88[ASN][1000 genomes]
rs10875121	0.82[ASN][1000 genomes]
rs11165935	0.82[ASN][1000 genomes]
rs11165937	0.82[ASN][1000 genomes]
rs12077442	0.82[ASN][1000 genomes]
rs1211661	0.81[AMR][1000 genomes]
rs1628294	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1702293	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17379561	0.82[ASN][1000 genomes]
rs2154402	0.96[AMR][1000 genomes]
rs2391903	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2802530	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2802531	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2802532	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28582591	0.82[ASN][1000 genomes]
rs28641479	0.82[ASN][1000 genomes]
rs4246515	0.82[ASN][1000 genomes]
rs4246516	0.82[ASN][1000 genomes]
rs4294451	0.88[ASN][1000 genomes]
rs4322261	0.88[ASN][1000 genomes]
rs4378243	0.94[ASN][1000 genomes]
rs4394694	0.82[ASN][1000 genomes]
rs4399192	0.82[ASN][1000 genomes]
rs4423049	0.83[ASN][1000 genomes]
rs4456128	0.88[ASN][1000 genomes]
rs4478846	0.94[ASN][1000 genomes]
rs4495746	0.80[ASN][1000 genomes]
rs4506495	0.82[ASN][1000 genomes]
rs4598523	0.83[ASN][1000 genomes]
rs4970725	0.88[ASN][1000 genomes]
rs61785881	0.82[ASN][1000 genomes]
rs61785883	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61785887	0.92[AMR][1000 genomes]
rs61785889	1.00[AFR][1000 genomes]
rs61785940	1.00[AFR][1000 genomes]
rs61786606	1.00[AFR][1000 genomes]
rs61786610	1.00[AFR][1000 genomes]
rs61786696	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs61786697	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs61787781	1.00[AFR][1000 genomes]
rs61787783	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61787784	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61787785	0.82[ASN][1000 genomes]
rs61787823	0.88[ASN][1000 genomes]
rs61787824	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61787826	0.82[ASN][1000 genomes]
rs61787827	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61787829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61787830	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61789073	1.00[AFR][1000 genomes]
rs61789075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61789077	0.82[ASN][1000 genomes]
rs61789078	0.82[ASN][1000 genomes]
rs61789079	0.82[ASN][1000 genomes]
rs61789082	0.82[ASN][1000 genomes]
rs6604098	0.83[ASN][1000 genomes]
rs72963738	0.82[ASN][1000 genomes]
rs7415086	0.88[ASN][1000 genomes]
rs9285628	0.82[ASN][1000 genomes]
rs9324379	0.82[ASN][1000 genomes]
rs9324380	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9659380	0.82[ASN][1000 genomes]
rs9662232	0.88[ASN][1000 genomes]
rs9662719	0.82[ASN][1000 genomes]
rs9662870	0.82[ASN][1000 genomes]
rs9727548	0.82[ASN][1000 genomes]
rs9727976	0.82[ASN][1000 genomes]
rs9729897	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830725	chr1:98257894-98443497	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv934244	chr1:98260729-98415915	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 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	chr1:98384000-98387600	Active TSS	Brain Substantia Nigra	brain
2	chr1:98384000-98387600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:98384200-98387400	Active TSS	Right Atrium	heart
4	chr1:98384200-98387400	Active TSS	GM12878-XiMat	blood
5	chr1:98384200-98387400	Active TSS	NHLF	lung
6	chr1:98384400-98387600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:98384400-98387600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:98384600-98387200	Active TSS	Psoas Muscle	Psoas
9	chr1:98384600-98387200	Active TSS	HSMMtube	muscle
10	chr1:98384600-98387400	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:98384800-98387000	Active TSS	Fetal Thymus	thymus
12	chr1:98384800-98387200	Active TSS	Aorta	Aorta
13	chr1:98384800-98387200	Active TSS	Colon Smooth Muscle	Colon
14	chr1:98384800-98387200	Active TSS	Left Ventricle	heart
15	chr1:98384800-98387200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr1:98384800-98387400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:98384800-98387400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:98384800-98387400	Active TSS	Brain Hippocampus Middle	brain
19	chr1:98384800-98387400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:98384800-98387400	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr1:98384800-98387600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:98384800-98387600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:98384800-98387600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:98384800-98387600	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:98385000-98387200	Active TSS	Primary T cells fromperipheralblood	blood
26	chr1:98385000-98387200	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr1:98385000-98387200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr1:98385000-98387200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:98385000-98387200	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr1:98385000-98387200	Active TSS	Brain Angular Gyrus	brain
31	chr1:98385000-98387200	Active TSS	Brain Cingulate Gyrus	brain
32	chr1:98385000-98387200	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr1:98385000-98387400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:98385000-98387400	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:98385000-98387400	Active TSS	Muscle Satellite Cultured Cells	--
36	chr1:98385000-98387400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:98385000-98387400	Active TSS	Brain Anterior Caudate	brain
38	chr1:98385000-98387400	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr1:98385000-98387400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:98385000-98387400	Active TSS	Duodenum Mucosa	Duodenum
41	chr1:98385000-98387400	Active TSS	Fetal Intestine Small	intestine
42	chr1:98385000-98387400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr1:98385000-98387400	Active TSS	Ovary	ovary
44	chr1:98385000-98387400	Active TSS	Right Ventricle	heart
45	chr1:98385000-98387400	Active TSS	Thymus	Thymus
46	chr1:98385000-98387400	Active TSS	Hela-S3	cervix
47	chr1:98385000-98387400	Active TSS	HSMM	muscle
48	chr1:98385000-98387400	Active TSS	NHDF-Ad	bronchial
49	chr1:98385000-98387600	Active TSS	A549	lung
50	chr1:98385200-98387000	Active TSS	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links