Variant report

Variant	rs2844793
Chromosome Location	chr6:30080496-30080497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr6:30080489-30081505	GM19193	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
2	SPI1	chr6:30080434-30080712	GM12878	blood:	n/a	n/a
3	RELA	chr6:30080467-30081547	GM12891	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
4	SPI1	chr6:30080409-30080633	GM12891	blood:	n/a	n/a
5	SPI1	chr6:30080424-30080585	K562	blood:	n/a	n/a
6	SPI1	chr6:30080365-30080726	GM12891	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30080495-30080545	HRCEpiC	kidney:	n/a
2	chr6:30080495-30080545	MCF10A-Er-Src	breast:	n/a
3	chr6:30080495-30080545	HEK293	kidney:	embryo
4	chr6:30080495-30080545	ProgFib	skin:	n/a
5	chr6:30080495-30080545	A549	lung:	n/a
6	chr6:30080495-30080545	PrEC	prostate:	n/a
7	chr6:30080495-30080545	AG04450	lung:	fetal
8	chr6:30080495-30080545	NHDF-neo	bronchial:	n/a
9	chr6:30080495-30080545	MCF-7	breast:	n/a
10	chr6:30080495-30080545	IMR90	lung:	fetal
11	chr6:30080495-30080545	HRE	kidney:	n/a
12	chr6:30080495-30080545	PANC-1	pancreas:	n/a
13	chr6:30080495-30080545	HEEpiC	esophagus:	n/a
14	chr6:30080495-30080545	AG09309	skin:	n/a
15	chr6:30080495-30080545	HCF	heart:	n/a
16	chr6:30080495-30080545	PFSK-1	brain:	n/a
17	chr6:30080495-30080545	HCM	heart:	n/a
18	chr6:30080495-30080545	HCT-116	colon:	n/a
19	chr6:30080495-30080545	H1-hESC	embryonic stem cell:	embryo
20	chr6:30080495-30080545	SK-N-SH_RA	brain:	n/a
21	chr6:30080495-30080545	AG09319	gingival:	n/a
22	chr6:30080495-30080545	HAEpiC	amniotic membrane:	n/a
23	chr6:30080495-30080545	SAEC	small airway:	n/a
24	chr6:30080495-30080545	GM19239	blood:	n/a
25	chr6:30080495-30080545	CMK	blood:	n/a
26	chr6:30080495-30080545	Hela-S3	cervix:	n/a
27	chr6:30080495-30080545	T-47D	breast:	n/a
28	chr6:30080495-30080545	NB4	blood:	n/a
29	chr6:30080495-30080545	LNCaP	prostate:	n/a
30	chr6:30080495-30080545	HIPEpiC	eye:	n/a
31	chr6:30080495-30080545	ovcar-3	ovarian:	n/a
32	chr6:30080495-30080545	Caco-2	colon:	n/a
33	chr6:30080495-30080545	AoSMC	blood vessel:	n/a
34	chr6:30080495-30080545	HL-60	blood:	n/a
35	chr6:30080495-30080545	ECC-1	luminal epithelium:	n/a
36	chr6:30080495-30080545	SKMC	muscle:	n/a
37	chr6:30080495-30080545	RPTEC	kidney:	n/a
38	chr6:30080495-30080545	HRPEpiC	eye:	n/a
39	chr6:30080495-30080545	GM12878	blood:	n/a
40	chr6:30080495-30080545	K562	blood:	n/a
41	chr6:30080495-30080545	BJ	skin:	n/a
42	chr6:30080495-30080545	HCPEpiC	choroid plexus:	n/a
43	chr6:30080495-30080545	HUVEC	blood vessel:	n/a
44	chr6:30080495-30080545	AG10803	skin:	n/a
45	chr6:30080495-30080545	GM12892	blood:	n/a
46	chr6:30080495-30080545	GM06990	blood:	n/a
47	chr6:30080495-30080545	HNPCEpiC	eye:	n/a
48	chr6:30080495-30080545	U87	brain:	n/a
49	chr6:30080495-30080545	HPAEpiC	pulmonary alveolar:	n/a
50	chr6:30080495-30080545	NHBE	bronchial:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:30072138..30074365-chr6:30079433..30082098,2	K562	blood:
2	chr6:30072893..30076173-chr6:30078690..30081417,3	MCF-7	breast:
3	chr6:30073473..30076763-chr6:30077230..30080756,3	K562	blood:

No data

Variant related genes	Relation type
TRIM31	TF binding region
TRIM31	CpG island
ENSG00000204616	Chromatin interaction
ENSG00000231226	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1034326	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1034327	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2239529	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245420	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2249099	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2427749	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517595	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517596	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517597	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517598	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2523976	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523977	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523979	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523981	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523982	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2523983	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523984	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2523985	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2523986	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523987	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523988	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523989	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523992	0.81[ASN][1000 genomes]
rs2844790	0.81[EUR][1000 genomes]
rs2844791	0.93[EUR][1000 genomes]
rs2844792	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884055	chr6:30078275-30087776	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2844793	ZKSCAN3	cis	parietal	SCAN
rs2844793	ZNF323	cis	parietal	SCAN
rs2844793	ZNF193	cis	cerebellum	SCAN
rs2844793	HIST1H3D	cis	parietal	SCAN
rs2844793	HIST1H3J	cis	parietal	SCAN
rs2844793	ZNF192	cis	cerebellum	SCAN
rs2844793	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2844793	ZNF192	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30078200-30080600	Active TSS	Stomach Mucosa	stomach
2	chr6:30078400-30081400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr6:30079200-30081000	Active TSS	Colonic Mucosa	Colon
4	chr6:30079400-30080600	Flanking Active TSS	Hela-S3	cervix
5	chr6:30080000-30080600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
6	chr6:30080000-30080600	Enhancers	Gastric	stomach
7	chr6:30080000-30080600	Active TSS	Rectal Smooth Muscle	rectum
8	chr6:30080000-30080800	Flanking Active TSS	Fetal Intestine Large	intestine
9	chr6:30080000-30081200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
10	chr6:30080000-30081800	Enhancers	Liver	Liver
11	chr6:30080200-30080600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr6:30080200-30080600	Enhancers	GM12878-XiMat	blood
13	chr6:30080200-30082400	Enhancers	HepG2	liver
14	chr6:30080400-30080600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
15	chr6:30080400-30080600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:30080400-30080600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:30080400-30080800	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr6:30080400-30080800	Flanking Active TSS	A549	lung

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