Variant report

Variant	rs6774950
Chromosome Location	chr3:101497925-101497926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:265)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:265 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:101497787-101497978	GM12891	blood:	n/a	n/a
2	SP4	chr3:101497698-101498162	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:101497797-101498323	HepG2	liver:	n/a	n/a
4	GATA3	chr3:101497712-101500022	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr3:101497892-101497945	Fibrobl	skin:	n/a	n/a
6	GATA1	chr3:101497706-101499394	PBDE	blood:	n/a	n/a
7	POLR2A	chr3:101497752-101498587	HEK293	kidney:	n/a	n/a
8	ZNF143	chr3:101497806-101498267	GM12878	blood:	n/a	chr3:101498215-101498225
9	CHD2	chr3:101497812-101498336	HepG2	liver:	n/a	chr3:101498006-101498016
10	SPI1	chr3:101497809-101498111	GM12891	blood:	n/a	n/a
11	RUNX3	chr3:101497270-101498658	GM12878	blood:	n/a	n/a
12	SP2	chr3:101497844-101498230	HepG2	liver:	n/a	n/a
13	SP2	chr3:101497786-101498158	H1-hESC	embryonic stem cell:	n/a	n/a
14	RCOR1	chr3:101497764-101498417	GM12878	blood:	n/a	n/a
15	MTA3	chr3:101497370-101497946	GM12878	blood:	n/a	n/a
16	CREB1	chr3:101497736-101498560	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:101497891-101498311	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr3:101497818-101498346	H1-hESC	embryonic stem cell:	n/a	n/a
19	MYC	chr3:101497673-101498331	NB4	blood:	n/a	chr3:101498268-101498278
20	EBF1	chr3:101497763-101497996	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:101497652-101498830	Gliobla	brain:	n/a	n/a
22	POLR2A	chr3:101497719-101498671	GM12878	blood:	n/a	n/a
23	HA-E2F1	chr3:101497285-101498904	MCF-7	breast:	n/a	chr3:101498008-101498017
24	E2F4	chr3:101497897-101498188	MCF10A-Er-Src	breast:	n/a	chr3:101498008-101498017
25	ELF1	chr3:101497715-101498638	GM12878	blood:	n/a	chr3:101498007-101498019
26	POLR2A	chr3:101497844-101497973	K562	blood:	n/a	n/a
27	RCOR1	chr3:101497904-101498387	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:101497723-101498716	GM15510	blood:	n/a	n/a
29	ELF1	chr3:101497781-101498274	HepG2	liver:	n/a	chr3:101498007-101498019
30	SP4	chr3:101497740-101498277	H1-hESC	embryonic stem cell:	n/a	n/a
31	BHLHE40	chr3:101497744-101498332	HepG2	liver:	n/a	chr3:101497975-101497991 chr3:101498202-101498218 chr3:101497972-101497988 chr3:101498210-101498226 chr3:101497883-101497899
32	YY1	chr3:101497655-101498457	HepG2	liver:	n/a	chr3:101498011-101498020 chr3:101498298-101498309
33	BACH1	chr3:101497541-101498103	H1-hESC	embryonic stem cell:	n/a	n/a
34	TCF12	chr3:101497674-101498238	ECC-1	luminal epithelium:	n/a	n/a
35	NR2F2	chr3:101497746-101498605	MCF-7	breast:	n/a	chr3:101498041-101498056
36	MXI1	chr3:101497543-101499227	IMR90	lung:	n/a	n/a
37	POLR2A	chr3:101497791-101498293	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:101497793-101498227	HepG2	liver:	n/a	n/a
39	POLR2A	chr3:101497738-101498736	A549	lung:	n/a	n/a
40	POLR2A	chr3:101497691-101498731	MCF-7	breast:	n/a	n/a
41	JUND	chr3:101497919-101498096	K562	blood:	n/a	n/a
42	MYC	chr3:101497836-101498021	MCF-7	breast:	n/a	n/a
43	ZBTB7A	chr3:101497770-101498536	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr3:101497673-101498819	U87	brain:	n/a	n/a
45	POLR2A	chr3:101497662-101498339	GM12878	blood:	n/a	n/a
46	MAX	chr3:101497763-101498140	K562	blood:	n/a	n/a
47	TAF1	chr3:101497725-101498310	HepG2	liver:	n/a	n/a
48	ZNF143	chr3:101497836-101498294	H1-hESC	embryonic stem cell:	n/a	chr3:101498215-101498225
49	MAFK	chr3:101497729-101498130	Hela-S3	cervix:	n/a	n/a
50	PAX5	chr3:101497736-101498306	GM12892	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:101497876-101497926	NH-A	brain:	n/a
2	chr3:101497876-101497926	RPTEC	kidney:	n/a
3	chr3:101497876-101497926	A549	lung:	n/a
4	chr3:101497876-101497926	AG09309	skin:	n/a
5	chr3:101497876-101497926	HRPEpiC	eye:	n/a
6	chr3:101497876-101497926	HCF	heart:	n/a
7	chr3:101497876-101497926	AG10803	skin:	n/a
8	chr3:101497876-101497926	HRCEpiC	kidney:	n/a
9	chr3:101497876-101497926	HCM	heart:	n/a
10	chr3:101497876-101497926	CMK	blood:	n/a
11	chr3:101497876-101497926	SK-N-SH	brain:	n/a
12	chr3:101497876-101497926	NT2-D1	testis:	n/a
13	chr3:101497876-101497926	AG04450	lung:	fetal
14	chr3:101497876-101497926	GM12878	blood:	n/a
15	chr3:101497876-101497926	HAEpiC	amniotic membrane:	n/a
16	chr3:101497876-101497926	HEEpiC	esophagus:	n/a
17	chr3:101497876-101497926	PFSK-1	brain:	n/a
18	chr3:101497876-101497926	AG09319	gingival:	n/a
19	chr3:101497876-101497926	HL-60	blood:	n/a
20	chr3:101497876-101497926	HCT-116	colon:	n/a
21	chr3:101497876-101497926	ProgFib	skin:	n/a
22	chr3:101497876-101497926	SK-N-SH_RA	brain:	n/a
23	chr3:101497876-101497926	ovcar-3	ovarian:	n/a
24	chr3:101497876-101497926	NHDF-neo	bronchial:	n/a
25	chr3:101497876-101497926	GM06990	blood:	n/a
26	chr3:101497876-101497926	HCPEpiC	choroid plexus:	n/a
27	chr3:101497876-101497926	HNPCEpiC	eye:	n/a
28	chr3:101497876-101497926	PANC-1	pancreas:	n/a
29	chr3:101497876-101497926	PrEC	prostate:	n/a
30	chr3:101497876-101497926	AG04449	skin:	fetal
31	chr3:101497876-101497926	HIPEpiC	eye:	n/a
32	chr3:101497876-101497926	HPAEpiC	pulmonary alveolar:	n/a
33	chr3:101497876-101497926	U87	brain:	n/a
34	chr3:101497876-101497926	HRE	kidney:	n/a
35	chr3:101497876-101497926	HUVEC	blood vessel:	n/a
36	chr3:101497876-101497926	NHBE	bronchial:	n/a
37	chr3:101497876-101497926	HMEC	breast:	n/a
38	chr3:101497876-101497926	Hela-S3	cervix:	n/a
39	chr3:101497876-101497926	NB4	blood:	n/a
40	chr3:101497876-101497926	IMR90	lung:	fetal
41	chr3:101497876-101497926	K562	blood:	n/a
42	chr3:101497876-101497926	Caco-2	colon:	n/a
43	chr3:101497876-101497926	AoSMC	blood vessel:	n/a
44	chr3:101497876-101497926	HepG2	liver:	n/a
45	chr3:101497876-101497926	T-47D	breast:	n/a
46	chr3:101497876-101497926	GM19239	blood:	n/a
47	chr3:101497876-101497926	H1-hESC	embryonic stem cell:	embryo
48	chr3:101497876-101497926	HEK293	kidney:	embryo
49	chr3:101497876-101497926	BJ	skin:	n/a
50	chr3:101497876-101497926	MCF10A-Er-Src	breast:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:101403905..101405852-chr3:101497702..101499506,2	MCF-7	breast:
2	chr3:101405192..101407713-chr3:101497187..101499121,2	MCF-7	breast:
3	chr3:101443470..101445204-chr3:101497641..101499611,2	MCF-7	breast:

No data

Variant related genes	Relation type
NXPE3	TF binding region
NXPE3	CpG island
ENSG00000182504	Chromatin interaction
ENSG00000114391	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11924203	0.82[EUR][1000 genomes]
rs2466369	0.82[YRI][hapmap]
rs2625289	0.92[YRI][hapmap]
rs41273611	0.82[EUR][1000 genomes]
rs6763679	0.82[EUR][1000 genomes]
rs6764700	0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6794860	0.82[EUR][1000 genomes]
rs6805496	0.82[EUR][1000 genomes]
rs6806256	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7613194	0.81[EUR][1000 genomes]
rs7644519	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6774950	FAM55C	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101497200-101498000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr3:101497200-101498000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr3:101497200-101498000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr3:101497200-101498000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:101497200-101498000	Flanking Active TSS	Dnd41	blood
6	chr3:101497200-101498000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:101497400-101498000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:101497400-101498000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:101497400-101498000	Flanking Active TSS	Primary B cells from peripheral blood	blood
10	chr3:101497400-101498000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr3:101497400-101498000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr3:101497400-101498000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:101497400-101498000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:101497400-101498000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:101497400-101498000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:101497400-101498000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr3:101497400-101498000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr3:101497400-101498000	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr3:101497400-101498000	Flanking Active TSS	Fetal Brain Female	brain
20	chr3:101497400-101498000	Flanking Active TSS	Fetal Intestine Small	intestine
21	chr3:101497400-101498000	Flanking Active TSS	Fetal Thymus	thymus
22	chr3:101497400-101498000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:101497400-101498000	Flanking Active TSS	GM12878-XiMat	blood
24	chr3:101497400-101498000	Flanking Active TSS	Hela-S3	cervix
25	chr3:101497400-101498000	Flanking Active TSS	K562	blood
26	chr3:101497400-101498000	Flanking Active TSS	NH-A	brain
27	chr3:101497400-101498000	Flanking Active TSS	Osteobl	bone
28	chr3:101497400-101498200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:101497400-101498800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:101497400-101498800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:101497400-101499000	Active TSS	Fetal Kidney	kidney
32	chr3:101497400-101499200	Active TSS	HSMMtube	muscle
33	chr3:101497400-101499800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:101497400-101500200	Active TSS	Psoas Muscle	Psoas
35	chr3:101497600-101498000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:101497600-101498000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:101497600-101498000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:101497600-101498000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr3:101497600-101498000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr3:101497600-101498000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr3:101497600-101498000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:101497600-101498000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:101497600-101498000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:101497600-101498000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:101497600-101498000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr3:101497600-101498000	Flanking Active TSS	Colonic Mucosa	Colon
47	chr3:101497600-101498000	Active TSS	Esophagus	oesophagus
48	chr3:101497600-101498000	Flanking Active TSS	Placenta	Placenta
49	chr3:101497600-101498000	Flanking Active TSS	Lung	lung
50	chr3:101497600-101498000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links