Variant report

Variant	rs2239529
Chromosome Location	chr6:30078330-30078331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30078118-30078367	HepG2	liver:	n/a	n/a
2	ZNF384	chr6:30078309-30078488	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30078290-30078340	SK-N-SH	brain:	n/a
2	chr6:30078290-30078340	BJ	skin:	n/a
3	chr6:30078290-30078340	BE2_C	brain:	n/a
4	chr6:30078290-30078340	CMK	blood:	n/a
5	chr6:30078290-30078340	HMEC	breast:	n/a
6	chr6:30078290-30078340	AG04449	skin:	fetal
7	chr6:30078290-30078340	ovcar-3	ovarian:	n/a
8	chr6:30078290-30078340	HCT-116	colon:	n/a
9	chr6:30078290-30078340	HIPEpiC	eye:	n/a
10	chr6:30078290-30078340	U87	brain:	n/a
11	chr6:30078290-30078340	MCF-7	breast:	n/a
12	chr6:30078290-30078340	NHBE	bronchial:	n/a
13	chr6:30078290-30078340	AG04450	lung:	fetal
14	chr6:30078290-30078340	NB4	blood:	n/a
15	chr6:30078290-30078340	Jurkat	blood:	n/a
16	chr6:30078290-30078340	HEK293	kidney:	embryo
17	chr6:30078290-30078340	HUVEC	blood vessel:	n/a
18	chr6:30078290-30078340	NT2-D1	testis:	n/a
19	chr6:30078290-30078340	SKMC	muscle:	n/a
20	chr6:30078290-30078340	IMR90	lung:	fetal
21	chr6:30078290-30078340	HepG2	liver:	n/a
22	chr6:30078290-30078340	Caco-2	colon:	n/a
23	chr6:30078290-30078340	HAEpiC	amniotic membrane:	n/a
24	chr6:30078290-30078340	SAEC	small airway:	n/a
25	chr6:30078290-30078340	Hela-S3	cervix:	n/a
26	chr6:30078290-30078340	GM19239	blood:	n/a
27	chr6:30078290-30078340	HCM	heart:	n/a
28	chr6:30078290-30078340	AG09309	skin:	n/a
29	chr6:30078290-30078340	HCPEpiC	choroid plexus:	n/a
30	chr6:30078290-30078340	H1-hESC	embryonic stem cell:	embryo
31	chr6:30078290-30078340	LNCaP	prostate:	n/a
32	chr6:30078290-30078340	AG10803	skin:	n/a
33	chr6:30078290-30078340	HCF	heart:	n/a
34	chr6:30078290-30078340	SK-N-SH_RA	brain:	n/a
35	chr6:30078290-30078340	ProgFib	skin:	n/a
36	chr6:30078290-30078340	RPTEC	kidney:	n/a
37	chr6:30078290-30078340	HRPEpiC	eye:	n/a
38	chr6:30078290-30078340	K562	blood:	n/a
39	chr6:30078290-30078340	A549	lung:	n/a
40	chr6:30078290-30078340	PANC-1	pancreas:	n/a
41	chr6:30078290-30078340	AG09319	gingival:	n/a
42	chr6:30078290-30078340	GM12878	blood:	n/a
43	chr6:30078290-30078340	AoSMC	blood vessel:	n/a
44	chr6:30078290-30078340	ECC-1	luminal epithelium:	n/a
45	chr6:30078290-30078340	GM12891	blood:	n/a
46	chr6:30078290-30078340	HRCEpiC	kidney:	n/a
47	chr6:30078290-30078340	HPAEpiC	pulmonary alveolar:	n/a
48	chr6:30078290-30078340	SK-N-MC	brain:	n/a
49	chr6:30078290-30078340	HL-60	blood:	n/a
50	chr6:30078290-30078340	T-47D	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	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

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1034326	0.87[EUR][1000 genomes]
rs1034327	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1541269	0.81[EUR][1000 genomes]
rs2245420	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2249099	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2427749	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517595	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517596	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517597	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517598	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2523976	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523977	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523979	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523981	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523982	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2523983	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523984	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2523985	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2523986	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523987	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523988	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523989	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523992	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2844790	0.82[EUR][1000 genomes]
rs2844791	0.94[EUR][1000 genomes]
rs2844792	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2844793	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs2239529	HIST1H3D	cis	parietal	SCAN
rs2239529	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2239529	HIST1H3J	cis	parietal	SCAN
rs2239529	ZNF193	cis	cerebellum	SCAN
rs2239529	ZNF192	cis	cerebellum	SCAN
rs2239529	ZKSCAN3	cis	parietal	SCAN
rs2239529	ZNF323	cis	parietal	SCAN
rs2239529	ZNF192	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30071600-30079200	Weak transcription	Gastric	stomach
2	chr6:30076000-30079400	Weak transcription	Hela-S3	cervix
3	chr6:30078000-30078400	Active TSS	Colonic Mucosa	Colon
4	chr6:30078000-30078400	ZNF genes & repeats	Fetal Intestine Small	intestine
5	chr6:30078000-30078400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr6:30078000-30078400	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr6:30078000-30078400	Active TSS	Rectal Smooth Muscle	rectum
8	chr6:30078200-30078400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
9	chr6:30078200-30078400	Bivalent Enhancer	Small Intestine	intestine
10	chr6:30078200-30078400	Enhancers	GM12878-XiMat	blood
11	chr6:30078200-30080600	Active TSS	Stomach Mucosa	stomach

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