Variant report

Variant	rs61642842
Chromosome Location	chr1:161128717-161128718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161128526-161129811	GM12892	blood:	n/a	n/a
2	MAX	chr1:161128553-161129981	A549	lung:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
3	MAZ	chr1:161128543-161129837	K562	blood:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
4	TCF12	chr1:161128485-161129676	A549	lung:	n/a	n/a
5	CTCF	chr1:161128680-161128830	BE2_C	brain:	n/a	chr1:161128786-161128804
6	TEAD4	chr1:161128334-161129348	K562	blood:	n/a	n/a
7	POLR2A	chr1:161128599-161129918	GM12878	blood:	n/a	n/a
8	MAX	chr1:161128410-161129925	K562	blood:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
9	REST	chr1:161128544-161130147	H1-neurons	neurons:	n/a	chr1:161129591-161129604
10	POLR2A	chr1:161128508-161129847	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr1:161128542-161129789	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:161128483-161130088	K562	blood:	n/a	n/a
13	POLR2A	chr1:161128632-161129754	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr1:161128626-161129829	PBDE	blood:	n/a	n/a
15	POLR2A	chr1:161128591-161129888	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr1:161128697-161129957	H1-hESC	embryonic stem cell:	n/a	chr1:161129194-161129208 chr1:161129303-161129323 chr1:161129309-161129321
17	POLR2A	chr1:161128624-161130284	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:161128619-161129877	H1-hESC	embryonic stem cell:	n/a	n/a
19	RCOR1	chr1:161128518-161129830	K562	blood:	n/a	n/a
20	POLR2A	chr1:161128525-161129891	K562	blood:	n/a	n/a
21	YY1	chr1:161128619-161129916	SK-N-SH	brain:	n/a	chr1:161129194-161129208 chr1:161129303-161129323 chr1:161129309-161129321
22	CEBPB	chr1:161128413-161128876	K562	blood:	n/a	n/a
23	POLR2A	chr1:161128573-161130479	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr1:161128536-161129996	HL-60	blood:	n/a	n/a
25	MYC	chr1:161128709-161128755	H1-hESC	embryonic stem cell:	n/a	n/a
26	CCNT2	chr1:161128589-161129716	K562	blood:	n/a	n/a
27	POLR2A	chr1:161128554-161130062	GM12892	blood:	n/a	n/a
28	POLR2A	chr1:161128701-161130357	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:161128604-161129807	MCF-7	breast:	n/a	n/a
30	POLR2A	chr1:161128568-161130055	K562	blood:	n/a	n/a
31	POLR2A	chr1:161128379-161130298	K562	blood:	n/a	n/a
32	TEAD4	chr1:161128406-161128820	K562	blood:	n/a	n/a
33	HCFC1	chr1:161128410-161130377	Hela-S3	cervix:	n/a	n/a
34	REST	chr1:161128627-161130041	A549	lung:	n/a	chr1:161129591-161129604
35	EGR1	chr1:161128361-161128728	K562	blood:	n/a	n/a
36	POLR2A	chr1:161128544-161130028	GM12892	blood:	n/a	n/a
37	POLR2A	chr1:161128335-161130429	K562	blood:	n/a	n/a
38	MAX	chr1:161128683-161129843	H1-hESC	embryonic stem cell:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
39	POLR2A	chr1:161128659-161129953	H1-hESC	embryonic stem cell:	n/a	n/a
40	MYC	chr1:161128524-161129711	K562	blood:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
41	POLR2A	chr1:161128550-161131005	SK-N-MC	brain:	n/a	n/a
42	SP1	chr1:161128577-161129511	A549	lung:	n/a	chr1:161129199-161129208 chr1:161129198-161129209 chr1:161129198-161129210 chr1:161129200-161129209
43	ZNF143	chr1:161128615-161129365	K562	blood:	n/a	n/a
44	POLR2A	chr1:161128188-161130127	H1-hESC	embryonic stem cell:	n/a	n/a
45	CBX3	chr1:161128303-161129860	K562	blood:	n/a	n/a
46	TAF1	chr1:161128688-161129958	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr1:161128465-161129283	K562	blood:	n/a	chr1:161128786-161128804
48	POLR2A	chr1:161128628-161129539	K562	blood:	n/a	n/a
49	CTCF	chr1:161128600-161128750	GM12870	blood:	n/a	n/a
50	POLR2A	chr1:161128410-161130469	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:161128717-161128767	ProgFib	skin:	n/a
2	chr1:161128717-161128767	SAEC	small airway:	n/a
3	chr1:161128717-161128767	BE2_C	brain:	n/a
4	chr1:161128717-161128767	HRPEpiC	eye:	n/a
5	chr1:161128717-161128767	GM12891	blood:	n/a
6	chr1:161128717-161128767	AG04449	skin:	fetal
7	chr1:161128717-161128767	T-47D	breast:	n/a
8	chr1:161128717-161128767	AG10803	skin:	n/a
9	chr1:161128717-161128767	HRCEpiC	kidney:	n/a
10	chr1:161128717-161128767	SK-N-MC	brain:	n/a
11	chr1:161128717-161128767	HAEpiC	amniotic membrane:	n/a
12	chr1:161128717-161128767	A549	lung:	n/a
13	chr1:161128717-161128767	NB4	blood:	n/a
14	chr1:161128717-161128767	Caco-2	colon:	n/a
15	chr1:161128717-161128767	RPTEC	kidney:	n/a
16	chr1:161128717-161128767	AoSMC	blood vessel:	n/a
17	chr1:161128717-161128767	CMK	blood:	n/a
18	chr1:161128717-161128767	ECC-1	luminal epithelium:	n/a
19	chr1:161128717-161128767	GM19239	blood:	n/a
20	chr1:161128717-161128767	Hepatocyte	liver:	n/a
21	chr1:161128717-161128767	K562	blood:	n/a
22	chr1:161128717-161128767	HUVEC	blood vessel:	n/a
23	chr1:161128717-161128767	HCPEpiC	choroid plexus:	n/a
24	chr1:161128717-161128767	SK-N-SH	brain:	n/a
25	chr1:161128717-161128767	Jurkat	blood:	n/a
26	chr1:161128717-161128767	GM12878	blood:	n/a
27	chr1:161128717-161128767	NHBE	bronchial:	n/a
28	chr1:161128717-161128767	H1-hESC	embryonic stem cell:	embryo
29	chr1:161128717-161128767	HPAEpiC	pulmonary alveolar:	n/a
30	chr1:161128717-161128767	HCT-116	colon:	n/a
31	chr1:161128717-161128767	AG09309	skin:	n/a
32	chr1:161128717-161128767	PrEC	prostate:	n/a
33	chr1:161128717-161128767	GM06990	blood:	n/a
34	chr1:161128717-161128767	PANC-1	pancreas:	n/a
35	chr1:161128717-161128767	LNCaP	prostate:	n/a
36	chr1:161128717-161128767	HepG2	liver:	n/a
37	chr1:161128717-161128767	HL-60	blood:	n/a
38	chr1:161128717-161128767	HIPEpiC	eye:	n/a
39	chr1:161128717-161128767	GM12892	blood:	n/a
40	chr1:161128717-161128767	MCF10A-Er-Src	breast:	n/a
41	chr1:161128717-161128767	HEEpiC	esophagus:	n/a
42	chr1:161128717-161128767	HEK293	kidney:	embryo
43	chr1:161128717-161128767	SKMC	muscle:	n/a
44	chr1:161128717-161128767	HRE	kidney:	n/a
45	chr1:161128717-161128767	AG04450	lung:	fetal
46	chr1:161128717-161128767	U87	brain:	n/a
47	chr1:161128717-161128767	PFSK-1	brain:	n/a
48	chr1:161128717-161128767	HCF	heart:	n/a
49	chr1:161128717-161128767	AG09319	gingival:	n/a
50	chr1:161128717-161128767	SK-N-SH_RA	brain:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161067905..161072134-chr1:161127935..161131211,3	MCF-7	breast:
2	chr1:160231832..160233674-chr1:161127837..161130606,2	MCF-7	breast:
3	chr1:161127350..161129092-chr1:161164865..161166799,2	MCF-7	breast:
4	chr1:160989787..160992592-chr1:161127591..161130267,2	K562	blood:
5	chr1:161101050..161105947-chr1:161126092..161130683,11	K562	blood:
6	chr1:161127959..161129889-chr1:161169079..161171967,3	K562	blood:
7	chr1:161085978..161089990-chr1:161127865..161134037,11	K562	blood:
8	chr1:161096487..161100046-chr1:161125256..161128979,4	K562	blood:
9	chr1:161052998..161054950-chr1:161128036..161130636,2	MCF-7	breast:
10	chr1:161126736..161129079-chr1:161368948..161371150,2	MCF-7	breast:
11	chr1:160989693..160991522-chr1:161127596..161130418,2	MCF-7	breast:
12	chr1:161101282..161104235-chr1:161127986..161130833,4	MCF-7	breast:
13	chr1:161085658..161090812-chr1:161125926..161133105,17	K562	blood:
14	chr1:161128018..161129911-chr1:161170467..161173789,3	K562	blood:

No data

Variant related genes	Relation type
USP21	TF binding region
USP21	CpG island
ENSG00000158859	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000132716	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000206921	Chromatin interaction
ENSG00000158769	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs34887199	1.00[AMR][1000 genomes]
rs55675252	1.00[AFR][1000 genomes]
rs55880062	1.00[AMR][1000 genomes]
rs56758346	1.00[AMR][1000 genomes]
rs57560345	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124643	0.83[AFR][1000 genomes]
rs74124646	0.83[AFR][1000 genomes]
rs74124647	1.00[AFR][1000 genomes]
rs74124650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124652	1.00[AMR][1000 genomes]
rs74124653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124672	1.00[AMR][1000 genomes]
rs74124691	1.00[AMR][1000 genomes]
rs74124697	1.00[AMR][1000 genomes]
rs74127620	1.00[AMR][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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 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	chr1:161124400-161128800	Weak transcription	Ovary	ovary
2	chr1:161124400-161129000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:161124400-161129000	Weak transcription	Aorta	Aorta
4	chr1:161125000-161128800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:161125200-161128800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:161126400-161128800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:161126400-161128800	Strong transcription	Thymus	Thymus
8	chr1:161127800-161128800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:161127800-161128800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:161128200-161128800	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:161128200-161128800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:161128200-161128800	Genic enhancers	Primary hematopoietic stem cells	blood
13	chr1:161128200-161128800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:161128200-161128800	Genic enhancers	Fetal Intestine Large	intestine
15	chr1:161128200-161128800	Genic enhancers	Fetal Intestine Small	intestine
16	chr1:161128200-161129000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:161128200-161129000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
18	chr1:161128400-161128800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:161128400-161128800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:161128400-161128800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:161128400-161128800	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr1:161128400-161128800	Enhancers	Liver	Liver
23	chr1:161128400-161128800	Enhancers	Colon Smooth Muscle	Colon
24	chr1:161128400-161128800	Enhancers	Fetal Heart	heart
25	chr1:161128400-161128800	Enhancers	Fetal Lung	lung
26	chr1:161128400-161128800	Genic enhancers	Fetal Muscle Leg	muscle
27	chr1:161128400-161128800	Genic enhancers	Placenta	Placenta
28	chr1:161128400-161128800	Genic enhancers	Fetal Thymus	thymus
29	chr1:161128400-161128800	Weak transcription	Right Ventricle	heart
30	chr1:161128400-161128800	Genic enhancers	Spleen	Spleen
31	chr1:161128400-161128800	Weak transcription	HUVEC	blood vessel
32	chr1:161128400-161128800	Transcr. at gene 5' and 3'	K562	blood
33	chr1:161128600-161128800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:161128600-161128800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:161128600-161128800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:161128600-161128800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:161128600-161128800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
38	chr1:161128600-161128800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:161128600-161128800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr1:161128600-161128800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:161128600-161128800	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:161128600-161128800	Genic enhancers	Primary B cells from cord blood	blood
43	chr1:161128600-161128800	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr1:161128600-161128800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:161128600-161128800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:161128600-161128800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:161128600-161128800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr1:161128600-161128800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:161128600-161128800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr1:161128600-161128800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links