Variant report

Variant	rs3778477
Chromosome Location	chr6:109776058-109776059
allele	C/G
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	YY1	chr6:109775774-109776592	GM12878	blood:	n/a	chr6:109776254-109776263
2	SPI1	chr6:109775811-109776240	HL-60	blood:	n/a	chr6:109776143-109776150
3	PAX5	chr6:109775796-109776200	GM12878	blood:	n/a	chr6:109776038-109776047 chr6:109776141-109776150
4	FOXM1	chr6:109775435-109776715	GM12878	blood:	n/a	n/a
5	BATF	chr6:109775888-109776289	GM12878	blood:	n/a	n/a
6	NFATC1	chr6:109775813-109776284	GM12878	blood:	n/a	n/a
7	MTA3	chr6:109775633-109776716	GM12878	blood:	n/a	n/a
8	CTCF	chr6:109775920-109776070	GM12878	blood:	n/a	n/a
9	RELA	chr6:109775808-109776470	GM19193	blood:	n/a	n/a
10	CTCF	chr6:109775940-109776090	AG04449	skin:	n/a	n/a
11	POU2F2	chr6:109775817-109776204	GM12878	blood:	n/a	n/a
12	EBF1	chr6:109775690-109776939	GM12878	blood:	n/a	n/a
13	ATF2	chr6:109775717-109776214	GM12878	blood:	n/a	n/a
14	KAT2A	chr6:109775958-109776068	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:109775787-109777267	IMR90	lung:	n/a	n/a
16	POLR2A	chr6:109775370-109776972	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:109774791-109778612	GM12892	blood:	n/a	n/a
18	ZNF143	chr6:109775869-109776160	GM12878	blood:	n/a	chr6:109775888-109775906
19	CTCF	chr6:109775940-109776090	AoAF	blood vessel:	n/a	n/a
20	SIN3A	chr6:109775640-109776879	GM12878	blood:	n/a	n/a
21	STAT5A	chr6:109775773-109776207	GM12878	blood:	n/a	chr6:109776179-109776191
22	BCLAF1	chr6:109775655-109776224	GM12878	blood:	n/a	chr6:109776038-109776047
23	POLR2A	chr6:109775261-109777757	GM19099	blood:	n/a	n/a
24	NFIC	chr6:109775502-109776367	GM12878	blood:	n/a	n/a
25	MTA3	chr6:109774944-109778262	GM12878	blood:	n/a	n/a
26	SP1	chr6:109775830-109776574	GM12878	blood:	n/a	chr6:109776249-109776258 chr6:109776248-109776257 chr6:109776252-109776264 chr6:109776253-109776267 chr6:109776254-109776263 chr6:109776252-109776264 chr6:109776253-109776262 chr6:109776248-109776258 chr6:109776253-109776263 chr6:109776253-109776262 chr6:109776247-109776259 chr6:109776248-109776257 chr6:109776247-109776259 chr6:109776253-109776263
27	POLR2A	chr6:109775300-109777378	NB4	blood:	n/a	n/a
28	REST	chr6:109775578-109777923	H1-neurons	neurons:	n/a	chr6:109776434-109776452 chr6:109777410-109777423 chr6:109775591-109775611 chr6:109777413-109777426 chr6:109775592-109775610
29	POLR2A	chr6:109775074-109777912	GM12878	blood:	n/a	n/a
30	RELA	chr6:109775723-109777443	GM10847	blood:	n/a	n/a
31	ELF1	chr6:109775739-109776203	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:109775718-109777473	H1-neurons	neurons:	n/a	n/a
33	CEBPB	chr6:109775931-109776174	GM12878	blood:	n/a	n/a
34	WRNIP1	chr6:109775511-109776164	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:109774855-109777633	GM12892	blood:	n/a	n/a
36	RELA	chr6:109775717-109777476	GM12892	blood:	n/a	n/a
37	POLR2A	chr6:109775827-109777653	H1-neurons	neurons:	n/a	n/a
38	MAX	chr6:109775363-109777255	NB4	blood:	n/a	chr6:109776320-109776330 chr6:109776227-109776237
39	SPI1	chr6:109775704-109776367	HL-60	blood:	n/a	chr6:109776143-109776150
40	ETS1	chr6:109775859-109776303	GM12878	blood:	n/a	chr6:109776136-109776150 chr6:109776254-109776265 chr6:109776138-109776149 chr6:109776142-109776149 chr6:109776168-109776179
41	SPI1	chr6:109775515-109776447	GM12878	blood:	n/a	chr6:109775647-109775656 chr6:109776143-109776150
42	SIN3A	chr6:109775713-109777875	H1-hESC	embryonic stem cell:	n/a	chr6:109777045-109777058 chr6:109777410-109777423
43	POLR2A	chr6:109775489-109777389	GM12892	blood:	n/a	n/a
44	MYC	chr6:109775925-109776084	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:109775374-109777341	GM12878	blood:	n/a	n/a
46	TCF12	chr6:109775695-109776431	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:109775685-109776235	GM12891	blood:	n/a	n/a
48	PAX5	chr6:109775649-109776969	GM12878	blood:	n/a	chr6:109776038-109776047 chr6:109776141-109776150
49	POLR2A	chr6:109775738-109777462	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:109774498-109777592	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:109774016..109776250-chr6:109801827..109803875,2	K562	blood:
2	chr6:109742234..109744237-chr6:109774891..109776518,2	MCF-7	breast:
3	chr6:109703058..109705958-chr6:109774873..109777253,2	MCF-7	breast:
4	chr6:109414902..109417715-chr6:109774468..109776378,2	K562	blood:
5	chr6:109702694..109704324-chr6:109775011..109776713,2	K562	blood:
6	chr6:109775795..109777582-chr6:109802976..109804493,2	MCF-7	breast:

Variant related genes	Relation type
MICAL1	TF binding region
ENSG00000080546	Chromatin interaction
ENSG00000112365	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10080429	0.88[EUR][1000 genomes]
rs1040284	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10457190	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10457192	0.85[ASN][1000 genomes]
rs10457194	0.82[ASN][1000 genomes]
rs10457195	0.80[ASN][1000 genomes]
rs1048203	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10782161	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782162	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782163	0.84[ASN][1000 genomes]
rs10872032	0.85[EUR][1000 genomes]
rs10872034	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153174	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11153175	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11153176	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11153177	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153180	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153181	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153183	0.85[ASN][1000 genomes]
rs11153188	0.80[ASN][1000 genomes]
rs11754455	0.85[ASN][1000 genomes]
rs11967108	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12190920	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12190996	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12192847	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193493	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12194061	0.80[ASN][1000 genomes]
rs12197114	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12197180	0.83[ASN][1000 genomes]
rs12198938	0.85[ASN][1000 genomes]
rs12199154	0.85[ASN][1000 genomes]
rs12206928	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12209691	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12212476	0.85[ASN][1000 genomes]
rs12213313	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524273	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12524639	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12528822	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13201951	0.82[ASN][1000 genomes]
rs13203587	0.85[ASN][1000 genomes]
rs13212766	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13220915	0.85[ASN][1000 genomes]
rs1322816	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1358997	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1358998	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1406899	0.85[ASN][1000 genomes]
rs1476388	0.84[ASN][1000 genomes]
rs1546980	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1590306	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17070580	0.88[EUR][1000 genomes]
rs1923725	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1998811	0.85[ASN][1000 genomes]
rs2024849	0.85[ASN][1000 genomes]
rs2024850	0.85[ASN][1000 genomes]
rs2024852	0.85[ASN][1000 genomes]
rs2024853	0.85[ASN][1000 genomes]
rs2236582	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2275650	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277114	0.85[ASN][1000 genomes]
rs34202013	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35056702	0.88[EUR][1000 genomes]
rs36035949	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36099706	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757234	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3778475	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3799839	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3807005	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818934	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59056467	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59906308	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68042406	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6906216	0.82[ASN][1000 genomes]
rs6911838	0.91[EUR][1000 genomes]
rs6916579	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6926096	0.82[ASN][1000 genomes]
rs6929023	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749517	0.84[ASN][1000 genomes]
rs752262	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755941	0.85[ASN][1000 genomes]
rs7773095	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7773950	0.85[ASN][1000 genomes]
rs9320287	0.88[EUR][1000 genomes]
rs9480933	0.84[EUR][1000 genomes]
rs9480948	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9480951	0.88[EUR][1000 genomes]
rs9480953	0.88[EUR][1000 genomes]
rs9480955	0.88[EUR][1000 genomes]
rs9480957	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487068	0.87[EUR][1000 genomes]
rs9487094	0.88[EUR][1000 genomes]
rs9487095	0.88[EUR][1000 genomes]
rs9487097	0.85[EUR][1000 genomes]
rs9487098	0.85[EUR][1000 genomes]
rs9487100	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9885646	0.88[EUR][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	esv3395145	chr6:109775784-109778832	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3778477	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs3778477	SMPD2	cis	Whole Blood	GTEx
rs3778477	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs3778477	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs3778477	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109768400-109776400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:109768400-109776400	Weak transcription	K562	blood
3	chr6:109775000-109776200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr6:109775000-109776200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
5	chr6:109775000-109776800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr6:109775000-109776800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:109775200-109776200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:109775200-109776200	Flanking Active TSS	Brain Cingulate Gyrus	brain
9	chr6:109775200-109776400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr6:109775200-109776400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:109775200-109776600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr6:109775200-109776600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr6:109775200-109776600	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr6:109775200-109778400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:109775400-109776200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:109775400-109776200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:109775400-109776200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr6:109775400-109776200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr6:109775400-109776200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:109775400-109776200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:109775400-109776200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:109775400-109776200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr6:109775400-109776200	Flanking Active TSS	Colonic Mucosa	Colon
24	chr6:109775400-109776200	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr6:109775400-109776200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr6:109775400-109776200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
27	chr6:109775400-109776200	Flanking Active TSS	Dnd41	blood
28	chr6:109775400-109776200	Flanking Active TSS	NH-A	brain
29	chr6:109775400-109776400	Flanking Active TSS	Fetal Muscle Trunk	muscle
30	chr6:109775400-109776800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:109775400-109777400	Active TSS	HSMM	muscle
32	chr6:109775400-109777600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:109775400-109777800	Active TSS	NHDF-Ad	bronchial
34	chr6:109775600-109776200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:109775600-109776200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr6:109775600-109776200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr6:109775600-109776200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:109775600-109776200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr6:109775600-109776200	Flanking Active TSS	Esophagus	oesophagus
40	chr6:109775600-109776200	Flanking Active TSS	Fetal Brain Male	brain
41	chr6:109775600-109776200	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr6:109775600-109776400	Flanking Active TSS	Thymus	Thymus
43	chr6:109775600-109776600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr6:109775600-109776800	Flanking Active TSS	Fetal Thymus	thymus
45	chr6:109775600-109776800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr6:109775600-109777600	Active TSS	Aorta	Aorta
47	chr6:109775600-109777800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr6:109775600-109778400	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr6:109775800-109776200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:109775800-109776200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links