Variant report

Variant	rs2249099
Chromosome Location	chr6:30079307-30079308
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:183)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30079265-30079315	HCF	heart:	n/a
2	chr6:30079265-30079315	PFSK-1	brain:	n/a
3	chr6:30079280-30079330	SAEC	small airway:	n/a
4	chr6:30079265-30079315	HepG2	liver:	n/a
5	chr6:30079307-30079357	HRCEpiC	kidney:	n/a
6	chr6:30079265-30079315	HCPEpiC	choroid plexus:	n/a
7	chr6:30079265-30079315	U87	brain:	n/a
8	chr6:30079265-30079315	HPAEpiC	pulmonary alveolar:	n/a
9	chr6:30079307-30079357	NHDF-neo	bronchial:	n/a
10	chr6:30079280-30079330	GM12891	blood:	n/a
11	chr6:30079265-30079315	GM12878	blood:	n/a
12	chr6:30079307-30079357	NT2-D1	testis:	n/a
13	chr6:30079307-30079357	HepG2	liver:	n/a
14	chr6:30079280-30079330	GM12892	blood:	n/a
15	chr6:30079280-30079330	Hela-S3	cervix:	n/a
16	chr6:30079265-30079315	A549	lung:	n/a
17	chr6:30079265-30079315	GM06990	blood:	n/a
18	chr6:30079265-30079315	HIPEpiC	eye:	n/a
19	chr6:30079280-30079330	Jurkat	blood:	n/a
20	chr6:30079265-30079315	AG04450	lung:	fetal
21	chr6:30079265-30079315	NB4	blood:	n/a
22	chr6:30079280-30079330	AG04449	skin:	fetal
23	chr6:30079307-30079357	Hela-S3	cervix:	n/a
24	chr6:30079307-30079357	SKMC	muscle:	n/a
25	chr6:30079307-30079357	HCM	heart:	n/a
26	chr6:30079280-30079330	T-47D	breast:	n/a
27	chr6:30079280-30079330	AG10803	skin:	n/a
28	chr6:30079265-30079315	HEK293	kidney:	embryo
29	chr6:30079265-30079315	H1-hESC	embryonic stem cell:	embryo
30	chr6:30079265-30079315	SK-N-SH	brain:	n/a
31	chr6:30079280-30079330	HPAEpiC	pulmonary alveolar:	n/a
32	chr6:30079307-30079357	GM06990	blood:	n/a
33	chr6:30079280-30079330	HL-60	blood:	n/a
34	chr6:30079280-30079330	Caco-2	colon:	n/a
35	chr6:30079280-30079330	NHDF-neo	bronchial:	n/a
36	chr6:30079280-30079330	Hepatocyte	liver:	n/a
37	chr6:30079265-30079315	AG09309	skin:	n/a
38	chr6:30079307-30079357	HCF	heart:	n/a
39	chr6:30079265-30079315	HCM	heart:	n/a
40	chr6:30079265-30079315	HCT-116	colon:	n/a
41	chr6:30079307-30079357	HRPEpiC	eye:	n/a
42	chr6:30079265-30079315	AG09319	gingival:	n/a
43	chr6:30079265-30079315	SK-N-SH_RA	brain:	n/a
44	chr6:30079265-30079315	IMR90	lung:	fetal
45	chr6:30079280-30079330	BJ	skin:	n/a
46	chr6:30079280-30079330	K562	blood:	n/a
47	chr6:30079265-30079315	HL-60	blood:	n/a
48	chr6:30079265-30079315	T-47D	breast:	n/a
49	chr6:30079280-30079330	AG09319	gingival:	n/a
50	chr6:30079307-30079357	BJ	skin:	n/a

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

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

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-5	chr6:30078995-30079520	NONHSAT108602

No data

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

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1034326	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1034327	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2239529	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245420	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2427749	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2517595	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2517596	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2517597	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2517598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523976	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523977	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523979	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523981	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523982	0.83[EUR][1000 genomes]
rs2523983	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523984	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523985	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523986	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523987	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523988	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523989	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844790	0.80[EUR][1000 genomes]
rs2844791	0.92[EUR][1000 genomes]
rs2844792	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2844793	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[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
rs2249099	ZNF192	cis	parietal	SCAN
rs2249099	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2249099	ZNF323	cis	parietal	SCAN
rs2249099	ZNF192	cis	cerebellum	SCAN
rs2249099	HIST1H3J	cis	parietal	SCAN
rs2249099	ZKSCAN3	cis	parietal	SCAN
rs2249099	ZNF193	cis	cerebellum	SCAN
rs2249099	HIST1H3D	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30076000-30079400	Weak transcription	Hela-S3	cervix
2	chr6:30078200-30080600	Active TSS	Stomach Mucosa	stomach
3	chr6:30078400-30080000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:30078400-30081400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr6:30079000-30080400	Bivalent/Poised TSS	Fetal Stomach	stomach
6	chr6:30079200-30079400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:30079200-30079400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:30079200-30079400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:30079200-30079400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
10	chr6:30079200-30079400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
11	chr6:30079200-30079400	Flanking Active TSS	Gastric	stomach
12	chr6:30079200-30080000	Active TSS	Duodenum Mucosa	Duodenum
13	chr6:30079200-30080000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
14	chr6:30079200-30080200	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr6:30079200-30081000	Active TSS	Colonic Mucosa	Colon

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