Variant report

Variant	rs55754437
Chromosome Location	chr4:2933031-2933032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:2932932-2934054	GM15510	blood:	n/a	n/a
2	POLR2A	chr4:2932773-2934678	GM12878	blood:	n/a	n/a
3	CTCF	chr4:2932920-2933070	BE2_C	brain:	n/a	n/a
4	POLR2A	chr4:2929559-2936017	GM12878	blood:	n/a	n/a
5	CTCF	chr4:2932980-2933130	SAEC	small airway:	n/a	n/a
6	POLR2A	chr4:2930254-2934156	A549	lung:	n/a	n/a
7	POLR2A	chr4:2932590-2935163	GM18505	blood:	n/a	n/a
8	POLR2A	chr4:2932331-2934648	K562	blood:	n/a	n/a
9	POLR2A	chr4:2932498-2933468	K562	blood:	n/a	n/a
10	POLR2A	chr4:2932946-2933208	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr4:2932566-2933774	A549	lung:	n/a	n/a
12	POLR2A	chr4:2932745-2933350	K562	blood:	n/a	n/a
13	POLR2A	chr4:2930058-2935267	GM12892	blood:	n/a	n/a
14	POLR2A	chr4:2932449-2934032	GM12891	blood:	n/a	n/a
15	POLR2A	chr4:2929805-2936295	HL-60	blood:	n/a	n/a
16	CCNT2	chr4:2932729-2933239	K562	blood:	n/a	n/a
17	POLR2A	chr4:2931859-2933573	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:2930022-2934363	GM12892	blood:	n/a	n/a
19	POLR2A	chr4:2932354-2934493	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:2932716-2934076	GM12892	blood:	n/a	n/a
21	POLR2A	chr4:2932480-2934004	GM12891	blood:	n/a	n/a
22	POLR2A	chr4:2932735-2936200	U87	brain:	n/a	n/a
23	POLR2A	chr4:2932716-2936132	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:2932520-2934181	GM12892	blood:	n/a	n/a
25	STAT5A	chr4:2932671-2934154	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:2930118-2940539	K562	blood:	n/a	n/a
27	POLR2A	chr4:2932494-2933996	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:2933007-2933404	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr4:2932094-2934114	HepG2	liver:	n/a	n/a
30	POLR2A	chr4:2932632-2933272	A549	lung:	n/a	n/a
31	POLR2A	chr4:2930179-2933129	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr4:2932797-2936194	U87	brain:	n/a	n/a
33	POLR2A	chr4:2932495-2934626	GM12891	blood:	n/a	n/a
34	POLR2A	chr4:2932896-2933186	ProgFib	skin:	n/a	n/a
35	POLR2A	chr4:2932421-2934495	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:2930571-2934637	PFSK-1	brain:	n/a	n/a
37	BCL3	chr4:2933027-2933971	GM12878	blood:	n/a	n/a
38	POLR2A	chr4:2931577-2935568	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr4:2932743-2935704	HepG2	liver:	n/a	n/a
40	POLR2A	chr4:2932939-2934051	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr4:2931820-2933264	MCF-7	breast:	n/a	n/a
42	POLR2A	chr4:2930108-2936184	GM12878	blood:	n/a	n/a
43	POLR2A	chr4:2930105-2936184	HL-60	blood:	n/a	n/a
44	POLR2A	chr4:2932413-2934316	GM19193	blood:	n/a	n/a
45	NFATC1	chr4:2932734-2934115	GM12878	blood:	n/a	n/a
46	MTA3	chr4:2932656-2935304	GM12878	blood:	n/a	n/a
47	CTCF	chr4:2932960-2933110	GM12869	blood:	n/a	n/a
48	HMGN3	chr4:2932994-2933060	K562	blood:	n/a	n/a
49	POLR2A	chr4:2932754-2933043	A549	lung:	n/a	n/a
50	POLR2A	chr4:2930406-2935196	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:2933016-2933066	HCT-116	colon:	n/a
2	chr4:2933016-2933066	HCPEpiC	choroid plexus:	n/a
3	chr4:2933016-2933066	GM06990	blood:	n/a
4	chr4:2933016-2933066	HAEpiC	amniotic membrane:	n/a
5	chr4:2933016-2933066	SAEC	small airway:	n/a
6	chr4:2933016-2933066	AG09319	gingival:	n/a
7	chr4:2933016-2933066	AG04449	skin:	fetal
8	chr4:2933016-2933066	GM12878	blood:	n/a
9	chr4:2933016-2933066	Hela-S3	cervix:	n/a
10	chr4:2933016-2933066	SK-N-SH	brain:	n/a
11	chr4:2933016-2933066	HRE	kidney:	n/a
12	chr4:2933016-2933066	HIPEpiC	eye:	n/a
13	chr4:2933016-2933066	AG10803	skin:	n/a
14	chr4:2933016-2933066	ProgFib	skin:	n/a
15	chr4:2933016-2933066	NHBE	bronchial:	n/a
16	chr4:2933016-2933066	HRCEpiC	kidney:	n/a
17	chr4:2933016-2933066	NT2-D1	testis:	n/a
18	chr4:2933016-2933066	SK-N-MC	brain:	n/a
19	chr4:2933016-2933066	BJ	skin:	n/a
20	chr4:2933016-2933066	HEK293	kidney:	embryo
21	chr4:2933016-2933066	CMK	blood:	n/a
22	chr4:2933016-2933066	PrEC	prostate:	n/a
23	chr4:2933016-2933066	HPAEpiC	pulmonary alveolar:	n/a
24	chr4:2933016-2933066	PANC-1	pancreas:	n/a
25	chr4:2933016-2933066	GM12891	blood:	n/a
26	chr4:2933016-2933066	HepG2	liver:	n/a
27	chr4:2933016-2933066	PFSK-1	brain:	n/a
28	chr4:2933016-2933066	Jurkat	blood:	n/a
29	chr4:2933016-2933066	GM19239	blood:	n/a
30	chr4:2933016-2933066	ECC-1	luminal epithelium:	n/a
31	chr4:2933016-2933066	IMR90	lung:	fetal
32	chr4:2933016-2933066	A549	lung:	n/a
33	chr4:2933016-2933066	H1-hESC	embryonic stem cell:	embryo
34	chr4:2933016-2933066	NH-A	brain:	n/a
35	chr4:2933016-2933066	NHDF-neo	bronchial:	n/a
36	chr4:2933016-2933066	GM12892	blood:	n/a
37	chr4:2933016-2933066	Hepatocyte	liver:	n/a
38	chr4:2933016-2933066	HEEpiC	esophagus:	n/a
39	chr4:2933016-2933066	AG04450	lung:	fetal
40	chr4:2933016-2933066	SKMC	muscle:	n/a
41	chr4:2933016-2933066	Caco-2	colon:	n/a
42	chr4:2933016-2933066	MCF10A-Er-Src	breast:	n/a
43	chr4:2933016-2933066	NB4	blood:	n/a
44	chr4:2933016-2933066	AG09309	skin:	n/a
45	chr4:2933016-2933066	RPTEC	kidney:	n/a
46	chr4:2933016-2933066	HCF	heart:	n/a
47	chr4:2933016-2933066	MCF-7	breast:	n/a
48	chr4:2933016-2933066	HNPCEpiC	eye:	n/a
49	chr4:2933016-2933066	HCM	heart:	n/a
50	chr4:2933016-2933066	HL-60	blood:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
2	chr4:2905536..2909706-chr4:2929255..2933631,5	MCF-7	breast:
3	chr4:2818050..2820446-chr4:2931198..2934919,4	MCF-7	breast:
4	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
5	chr4:2866956..2870306-chr4:2932983..2937533,4	K562	blood:
6	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
7	chr4:2798213..2801828-chr4:2930948..2933812,4	MCF-7	breast:
8	chr4:2747787..2749353-chr4:2932713..2934414,2	MCF-7	breast:
9	chr4:2900149..2902689-chr4:2931088..2933616,2	MCF-7	breast:
10	chr4:2844667..2846499-chr4:2932403..2934582,2	MCF-7	breast:

No data

Variant related genes	Relation type
NOP14-AS1	TF binding region
NOP14-AS1	CpG island
ENSG00000168884	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1014947	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1014948	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12623	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12643323	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12647647	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12647713	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12649553	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16843589	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16843603	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17833981	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17834203	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3021131	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59150074	0.81[EUR][1000 genomes]
rs6824567	0.81[EUR][1000 genomes]
rs7436306	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs55754437	GRK4	cis	Thyroid	GTEx
rs55754437	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs55754437	GRK4	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
2	chr4:2907400-2935400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:2911200-2935000	Weak transcription	Psoas Muscle	Psoas
4	chr4:2912600-2934800	Weak transcription	A549	lung
5	chr4:2913000-2935000	Weak transcription	K562	blood
6	chr4:2923800-2933600	Strong transcription	Thymus	Thymus
7	chr4:2924000-2934400	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:2924200-2934400	Strong transcription	Fetal Stomach	stomach
9	chr4:2924200-2934800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:2924400-2933800	Strong transcription	Fetal Brain Female	brain
11	chr4:2924400-2934200	Strong transcription	Brain Germinal Matrix	brain
12	chr4:2924800-2933600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:2925000-2933800	Strong transcription	Dnd41	blood
14	chr4:2925000-2934400	Strong transcription	Osteobl	bone
15	chr4:2925200-2933200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:2925200-2933400	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr4:2925200-2934800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:2925400-2933200	Strong transcription	HSMMtube	muscle
19	chr4:2925400-2933400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:2925400-2934400	Strong transcription	NHLF	lung
21	chr4:2925600-2933200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:2925600-2933800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:2925600-2934200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:2925600-2934400	Strong transcription	NHEK	skin
25	chr4:2925800-2934200	Strong transcription	Esophagus	oesophagus
26	chr4:2925800-2935000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:2926000-2933200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:2926000-2933200	Strong transcription	Aorta	Aorta
29	chr4:2926000-2933600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:2926000-2934200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:2926000-2934400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:2926200-2935000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:2926400-2933200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:2926600-2934600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr4:2926600-2935200	Weak transcription	Fetal Kidney	kidney
36	chr4:2926600-2936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr4:2927000-2933200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:2927000-2934400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:2927200-2934400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:2927400-2933600	Strong transcription	Brain Anterior Caudate	brain
41	chr4:2927600-2934400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr4:2928200-2934000	Weak transcription	Fetal Brain Male	brain
43	chr4:2928600-2935000	Weak transcription	Small Intestine	intestine
44	chr4:2928600-2935200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:2928800-2933200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:2930000-2934800	Weak transcription	NHDF-Ad	bronchial
47	chr4:2930400-2933800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:2930400-2934200	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr4:2930400-2934400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:2930600-2933800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links