Variant report

Variant	rs9838388
Chromosome Location	chr3:42743144-42743145
allele	C/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	ELK1	chr3:42743089-42743217	Hela-S3	cervix:	n/a	n/a
2	REST	chr3:42742575-42743626	MCF-7	breast:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
3	ZNF143	chr3:42742800-42743308	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr3:42743010-42743171	K562	blood:	n/a	n/a
5	CTCF	chr3:42743089-42743237	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr3:42742834-42743341	ECC-1	luminal epithelium:	n/a	chr3:42743016-42743030 chr3:42743015-42743029
7	REST	chr3:42742554-42743609	GM12878	blood:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
8	RCOR1	chr3:42742965-42743220	GM12878	blood:	n/a	n/a
9	MAZ	chr3:42742973-42743260	GM12878	blood:	n/a	n/a
10	CTCF	chr3:42743100-42743250	HCM	heart:	n/a	n/a
11	GABPA	chr3:42742908-42743246	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr3:42742865-42743370	PFSK-1	brain:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
13	REST	chr3:42742904-42743238	SK-N-SH	brain:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
14	CTCF	chr3:42743100-42743250	HVMF	connective:	n/a	n/a
15	MAX	chr3:42742987-42743159	Hela-S3	cervix:	n/a	n/a
16	REST	chr3:42743062-42743188	PANC-1	pancreas:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
17	CTCF	chr3:42743000-42743150	RPTEC	kidney:	n/a	chr3:42743019-42743032
18	HCFC1	chr3:42742956-42743276	K562	blood:	n/a	n/a
19	CTCF	chr3:42743100-42743250	K562	blood:	n/a	n/a
20	ETS1	chr3:42742920-42743235	K562	blood:	n/a	n/a
21	CTCF	chr3:42742978-42743247	K562	blood:	n/a	chr3:42743019-42743032
22	MAZ	chr3:42742779-42743374	IMR90	lung:	n/a	n/a
23	MAX	chr3:42742942-42743235	NB4	blood:	n/a	n/a
24	ELF1	chr3:42742937-42743197	K562	blood:	n/a	n/a
25	REST	chr3:42742581-42743686	A549	lung:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
26	YY1	chr3:42743021-42743162	K562	blood:	n/a	n/a
27	YY1	chr3:42742908-42743204	H1-hESC	embryonic stem cell:	n/a	n/a
28	NR2F2	chr3:42742954-42743220	K562	blood:	n/a	n/a
29	REST	chr3:42742683-42743525	H1-hESC	embryonic stem cell:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
30	MXI1	chr3:42742990-42743196	H1-hESC	embryonic stem cell:	n/a	n/a
31	SIN3AK20	chr3:42742949-42743164	K562	blood:	n/a	n/a
32	CTCF	chr3:42743062-42743242	K562	blood:	n/a	n/a
33	REST	chr3:42742752-42743422	PANC-1	pancreas:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
34	REST	chr3:42742650-42743678	PANC-1	pancreas:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
35	CTCF	chr3:42743136-42743227	GM12878	blood:	n/a	n/a
36	RCOR1	chr3:42742938-42743351	HepG2	liver:	n/a	n/a
37	REST	chr3:42742608-42743688	PFSK-1	brain:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
38	CTCF	chr3:42743080-42743230	GM06990	blood:	n/a	n/a
39	CEBPB	chr3:42742992-42743190	H1-hESC	embryonic stem cell:	n/a	n/a
40	BHLHE40	chr3:42742936-42743229	K562	blood:	n/a	n/a
41	CTCF	chr3:42743060-42743210	HBMEC	blood vessel:	n/a	n/a
42	TEAD4	chr3:42742801-42743463	A549	lung:	n/a	n/a
43	REST	chr3:42742434-42743712	PFSK-1	brain:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
44	REST	chr3:42742654-42743858	HCT-116	colon:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
45	REST	chr3:42742747-42743632	MCF-7	breast:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126
46	JUND	chr3:42742967-42743160	K562	blood:	n/a	n/a
47	ZNF143	chr3:42742943-42743286	K562	blood:	n/a	n/a
48	ZBTB7A	chr3:42743013-42743185	K562	blood:	n/a	n/a
49	CTCF	chr3:42743060-42743210	HRE	kidney:	n/a	n/a
50	REST	chr3:42742831-42743305	SK-N-SH	brain:	n/a	chr3:42743107-42743127 chr3:42743110-42743123 chr3:42743107-42743127 chr3:42743113-42743127 chr3:42743107-42743127 chr3:42743117-42743125 chr3:42743107-42743120 chr3:42743107-42743116 chr3:42743112-42743121 chr3:42743108-42743126

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42737037..42739602-chr3:42741625..42745097,3	K562	blood:
2	chr3:42724857..42728583-chr3:42742957..42746730,4	K562	blood:

Variant related genes	Relation type
HHATL-AS1	TF binding region
HHATL	TF binding region
ENSG00000010282	Chromatin interaction
ENSG00000157119	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10461012	0.90[EUR][1000 genomes]
rs10865920	0.87[EUR][1000 genomes]
rs10865921	0.87[EUR][1000 genomes]
rs10865923	0.82[EUR][1000 genomes]
rs11129969	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs11129970	0.88[EUR][1000 genomes]
rs11709054	0.85[EUR][1000 genomes]
rs11709500	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs11713172	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs11915803	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs17074778	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs17238314	0.88[EUR][1000 genomes]
rs17238798	0.83[EUR][1000 genomes]
rs2240861	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs34110933	0.85[EUR][1000 genomes]
rs55884426	0.88[EUR][1000 genomes]
rs55904344	0.86[EUR][1000 genomes]
rs59478814	0.87[EUR][1000 genomes]
rs59713146	0.88[EUR][1000 genomes]
rs60049195	0.87[EUR][1000 genomes]
rs60176972	0.87[EUR][1000 genomes]
rs62246603	0.86[EUR][1000 genomes]
rs62246606	0.85[EUR][1000 genomes]
rs62250113	0.90[EUR][1000 genomes]
rs62250114	0.90[EUR][1000 genomes]
rs6442057	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs9836162	0.94[CEU][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837412	0.90[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42738800-42743600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr3:42739200-42751800	Weak transcription	Pancreas	Pancrea
3	chr3:42740800-42744200	Active TSS	Left Ventricle	heart
4	chr3:42741200-42744400	Active TSS	Right Ventricle	heart
5	chr3:42742000-42743600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr3:42742000-42744200	Flanking Active TSS	Brain Substantia Nigra	brain
7	chr3:42742000-42744200	Active TSS	Right Atrium	heart
8	chr3:42742000-42744800	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr3:42742000-42745000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:42742200-42744200	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr3:42742400-42743200	Active TSS	Psoas Muscle	Psoas
12	chr3:42742400-42744200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:42742400-42744800	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr3:42742600-42743400	Enhancers	Hela-S3	cervix
15	chr3:42742600-42743600	Enhancers	HSMMtube	muscle
16	chr3:42742600-42743800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:42742600-42744000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:42742600-42744000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:42742800-42743200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:42742800-42743200	Enhancers	Aorta	Aorta
21	chr3:42742800-42743400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:42742800-42743400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:42742800-42743400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:42742800-42743400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:42742800-42743400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:42742800-42743400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr3:42742800-42743400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:42742800-42743400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:42742800-42743400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:42742800-42743400	Enhancers	Gastric	stomach
31	chr3:42742800-42743600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:42742800-42743600	Bivalent Enhancer	Placenta	Placenta
33	chr3:42742800-42743600	Enhancers	Lung	lung
34	chr3:42742800-42743600	Enhancers	HMEC	breast
35	chr3:42742800-42745000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:42743000-42743200	Enhancers	Fetal Heart	heart
37	chr3:42743000-42743200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr3:42743000-42743200	Enhancers	Fetal Muscle Leg	muscle
39	chr3:42743000-42743400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr3:42743000-42743400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:42743000-42743400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:42743000-42743400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:42743000-42743400	Active TSS	Brain Angular Gyrus	brain
44	chr3:42743000-42743600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:42743000-42743600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:42743000-42744800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:42743000-42745000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr3:42743000-42746000	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links