Variant report

Variant	rs6104943
Chromosome Location	chr20:1317816-1317817
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	STAT3	chr20:1317604-1317873	MCF10A-Er-Src	breast:	n/a	chr20:1317675-1317687 chr20:1317796-1317804
2	POLR2A	chr20:1317571-1318056	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr20:1317637-1317884	A549	lung:	n/a	n/a
4	POLR2A	chr20:1317311-1317916	K562	blood:	n/a	n/a
5	POLR2A	chr20:1317276-1317899	GM12878	blood:	n/a	n/a
6	POLR2A	chr20:1317481-1317990	MCF10A-Er-Src	breast:	n/a	n/a
7	ELF1	chr20:1317341-1317914	GM12878	blood:	n/a	n/a
8	NFIC	chr20:1316864-1318084	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr20:1317633-1318005	HUVEC	blood vessel:	n/a	n/a
10	NFIC	chr20:1316950-1318125	ECC-1	luminal epithelium:	n/a	n/a
11	EP300	chr20:1317277-1318171	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr20:1312270-1318121	SK-N-MC	brain:	n/a	n/a
13	MAX	chr20:1317330-1318015	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr20:1316600-1318859	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr20:1317614-1317864	A549	lung:	n/a	n/a
16	POLR2A	chr20:1316783-1318120	HUVEC	blood vessel:	n/a	n/a
17	FOS	chr20:1316736-1318217	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr20:1316669-1317977	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr20:1317542-1318040	K562	blood:	n/a	n/a
20	TEAD4	chr20:1317444-1318027	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr20:1316380-1318112	HepG2	liver:	n/a	n/a
22	POLR2A	chr20:1316567-1318878	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr20:1316652-1318018	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr20:1317348-1317932	A549	lung:	n/a	n/a
25	POLR2A	chr20:1316760-1318230	HUVEC	blood vessel:	n/a	n/a
26	NR3C1	chr20:1317665-1317892	ECC-1	luminal epithelium:	n/a	n/a
27	STAT3	chr20:1317572-1317863	MCF10A-Er-Src	breast:	n/a	chr20:1317675-1317687 chr20:1317796-1317804
28	YY1	chr20:1317423-1317954	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr20:1317318-1318855	PFSK-1	brain:	n/a	n/a
30	JUN	chr20:1317501-1318306	HUVEC	blood vessel:	n/a	n/a
31	STAT3	chr20:1317602-1317872	MCF10A-Er-Src	breast:	n/a	chr20:1317675-1317687 chr20:1317796-1317804
32	TCF12	chr20:1317393-1318104	ECC-1	luminal epithelium:	n/a	chr20:1317675-1317685
33	POLR2A	chr20:1316565-1318243	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr20:1317606-1317881	A549	lung:	n/a	n/a
35	POLR2A	chr20:1316556-1317856	K562	blood:	n/a	n/a
36	ZNF263	chr20:1317208-1317841	HEK293-T-REx	kidney:	n/a	n/a
37	POLR2A	chr20:1316571-1319942	K562	blood:	n/a	n/a
38	MYC	chr20:1317625-1317842	MCF10A-Er-Src	breast:	n/a	n/a
39	GATA2	chr20:1316710-1318218	HUVEC	blood vessel:	n/a	chr20:1317405-1317417 chr20:1317407-1317415
40	POLR2A	chr20:1317731-1317838	MCF-7	breast:	n/a	n/a
41	POLR2A	chr20:1317363-1318420	ECC-1	luminal epithelium:	n/a	n/a
42	STAT3	chr20:1317636-1317836	MCF10A-Er-Src	breast:	n/a	chr20:1317675-1317687 chr20:1317796-1317804
43	TCF12	chr20:1317382-1318093	ECC-1	luminal epithelium:	n/a	chr20:1317675-1317685
44	POLR2A	chr20:1316797-1317956	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr20:1316715-1318118	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr20:1317721-1318248	HepG2	liver:	n/a	n/a
47	POLR2A	chr20:1316780-1318388	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1309326..1311683-chr20:1317369..1320859,3	MCF-7	breast:
2	chr20:1307820..1310838-chr20:1317476..1319823,3	K562	blood:

Variant related genes	Relation type
ENSG00000203630	TF binding region
ENSG00000125775	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs57806058	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6109511	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6109522	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73579400	0.81[AFR][1000 genomes]
rs73581208	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8117744	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8119259	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1307400-1319000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr20:1307600-1327200	Weak transcription	Fetal Brain Female	brain
3	chr20:1307600-1340400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:1307800-1319400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr20:1308800-1318000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr20:1309000-1322000	Weak transcription	HSMMtube	muscle
7	chr20:1309800-1335400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr20:1310000-1348800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr20:1310200-1321400	Weak transcription	K562	blood
10	chr20:1311600-1335200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr20:1311800-1318200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr20:1313800-1327200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr20:1314200-1318200	Weak transcription	Placenta	Placenta
14	chr20:1314200-1320000	Enhancers	HUVEC	blood vessel
15	chr20:1314400-1319200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:1314400-1325600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr20:1314600-1318600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr20:1314600-1319600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr20:1314600-1327200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:1314800-1319200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr20:1314800-1322000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr20:1314800-1327200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr20:1315000-1319600	Strong transcription	Fetal Intestine Small	intestine
24	chr20:1315000-1327600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:1315200-1318000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:1315400-1319200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr20:1315400-1319600	Enhancers	Adipose Nuclei	Adipose
28	chr20:1315600-1318200	Weak transcription	Fetal Stomach	stomach
29	chr20:1315600-1329200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr20:1316000-1318400	Enhancers	NHEK	skin
31	chr20:1316000-1325600	Weak transcription	A549	lung
32	chr20:1316200-1318400	Weak transcription	HepG2	liver
33	chr20:1316200-1327200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr20:1316600-1318000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr20:1316600-1318200	Enhancers	HMEC	breast
36	chr20:1316600-1318400	Enhancers	Liver	Liver
37	chr20:1316600-1318400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr20:1316600-1318800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr20:1316600-1319000	Enhancers	Stomach Mucosa	stomach
40	chr20:1316600-1319800	Enhancers	Right Atrium	heart
41	chr20:1316600-1320800	Enhancers	Left Ventricle	heart
42	chr20:1316800-1318000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr20:1316800-1318600	Enhancers	Stomach Smooth Muscle	stomach
44	chr20:1316800-1318800	Enhancers	Gastric	stomach
45	chr20:1316800-1319000	Enhancers	Esophagus	oesophagus
46	chr20:1316800-1319200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr20:1316800-1319600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr20:1316800-1319600	Enhancers	Lung	lung
49	chr20:1316800-1319600	Enhancers	Spleen	Spleen
50	chr20:1316800-1319800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links