Variant report

Variant	rs2844796
Chromosome Location	chr6:30072511-30072512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:30072500-30072650	HAc	cerebellar:	n/a	n/a
2	CTCF	chr6:30072380-30072530	HCM	heart:	n/a	n/a
3	RAD21	chr6:30072511-30072838	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr6:30072500-30072650	HUVEC	blood vessel:	n/a	n/a
5	CTCF	chr6:30072500-30072650	HRPEpiC	eye:	n/a	n/a
6	RAD21	chr6:30072467-30072800	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr6:30072480-30072630	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr6:30072501-30072718	HepG2	liver:	n/a	n/a
9	CTCF	chr6:30072500-30072650	HPAF	blood vessel:	n/a	n/a
10	CTCF	chr6:30072485-30072772	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr6:30072460-30072610	HCT-116	colon:	n/a	n/a
12	CTCF	chr6:30072480-30072630	MCF-7	breast:	n/a	n/a
13	CTCF	chr6:30072509-30072723	HepG2	liver:	n/a	n/a
14	CTCF	chr6:30072494-30072725	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30072468-30072518	GM12892	blood:	n/a
2	chr6:30072468-30072518	GM12878	blood:	n/a
3	chr6:30072468-30072518	AG09319	gingival:	n/a
4	chr6:30072468-30072518	HCT-116	colon:	n/a
5	chr6:30072468-30072518	HRE	kidney:	n/a
6	chr6:30072468-30072518	IMR90	lung:	fetal
7	chr6:30072468-30072518	ProgFib	skin:	n/a
8	chr6:30072468-30072518	MCF-7	breast:	n/a
9	chr6:30072468-30072518	HRPEpiC	eye:	n/a
10	chr6:30072468-30072518	NHBE	bronchial:	n/a
11	chr6:30072468-30072518	NB4	blood:	n/a
12	chr6:30072468-30072518	HNPCEpiC	eye:	n/a
13	chr6:30072468-30072518	HEK293	kidney:	embryo
14	chr6:30072468-30072518	HAEpiC	amniotic membrane:	n/a
15	chr6:30072468-30072518	Jurkat	blood:	n/a
16	chr6:30072468-30072518	HPAEpiC	pulmonary alveolar:	n/a
17	chr6:30072468-30072518	PFSK-1	brain:	n/a
18	chr6:30072468-30072518	K562	blood:	n/a
19	chr6:30072468-30072518	HCPEpiC	choroid plexus:	n/a
20	chr6:30072468-30072518	HepG2	liver:	n/a
21	chr6:30072468-30072518	Hela-S3	cervix:	n/a
22	chr6:30072468-30072518	AG09309	skin:	n/a
23	chr6:30072468-30072518	ovcar-3	ovarian:	n/a
24	chr6:30072468-30072518	AG04449	skin:	fetal
25	chr6:30072468-30072518	MCF10A-Er-Src	breast:	n/a
26	chr6:30072468-30072518	PANC-1	pancreas:	n/a
27	chr6:30072468-30072518	HEEpiC	esophagus:	n/a
28	chr6:30072468-30072518	NT2-D1	testis:	n/a
29	chr6:30072468-30072518	SK-N-SH_RA	brain:	n/a
30	chr6:30072468-30072518	RPTEC	kidney:	n/a
31	chr6:30072468-30072518	GM06990	blood:	n/a
32	chr6:30072468-30072518	U87	brain:	n/a
33	chr6:30072468-30072518	AG04450	lung:	fetal
34	chr6:30072468-30072518	AoSMC	blood vessel:	n/a
35	chr6:30072468-30072518	Hepatocyte	liver:	n/a
36	chr6:30072468-30072518	SK-N-MC	brain:	n/a
37	chr6:30072468-30072518	NH-A	brain:	n/a
38	chr6:30072468-30072518	BE2_C	brain:	n/a
39	chr6:30072468-30072518	CMK	blood:	n/a
40	chr6:30072468-30072518	Caco-2	colon:	n/a
41	chr6:30072468-30072518	BJ	skin:	n/a
42	chr6:30072468-30072518	T-47D	breast:	n/a
43	chr6:30072468-30072518	ECC-1	luminal epithelium:	n/a
44	chr6:30072468-30072518	H1-hESC	embryonic stem cell:	embryo
45	chr6:30072468-30072518	GM12891	blood:	n/a
46	chr6:30072468-30072518	SAEC	small airway:	n/a
47	chr6:30072468-30072518	HRCEpiC	kidney:	n/a
48	chr6:30072468-30072518	HIPEpiC	eye:	n/a
49	chr6:30072468-30072518	AG10803	skin:	n/a
50	chr6:30072468-30072518	PrEC	prostate:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30070301..30072986-chr6:30097734..30100221,43	MCF-7	breast:
2	chr6:30071292..30074099-chr6:30075439..30077084,2	K562	blood:
3	chr6:30027872..30030809-chr6:30069511..30072907,4	K562	blood:
4	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
5	chr6:30072138..30074365-chr6:30079433..30082098,2	K562	blood:

No data

Variant related genes	Relation type
TRIM31-AS1	TF binding region
TRIM31-AS1	CpG island
ENSG00000204616	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1108052	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1108053	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1110446	0.81[EUR][1000 genomes]
rs1110448	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1116221	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1116222	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1264694	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1264695	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1264696	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1264702	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2072110	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2240071	0.81[EUR][1000 genomes]
rs2248289	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523994	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2524005	1.00[CEU][hapmap]
rs6457149	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6915823	0.83[AFR][1000 genomes]
rs916569	0.88[AMR][1000 genomes];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	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2844796	HIST1H2AM	cis	parietal	SCAN
rs2844796	HIST1H2BM	cis	cerebellum	SCAN
rs2844796	HIST1H4G	cis	cerebellum	SCAN
rs2844796	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2844796	ZNF323	cis	parietal	SCAN
rs2844796	HIST1H2BN	cis	parietal	SCAN
rs2844796	ZKSCAN3	cis	parietal	SCAN
rs2844796	NA	cis	multi-tissue	Pritchard
rs2844796	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2844796	ZSCAN23	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30068000-30072600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:30070000-30075400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:30071400-30073200	Enhancers	Hela-S3	cervix
4	chr6:30071600-30079200	Weak transcription	Gastric	stomach
5	chr6:30071800-30072800	Enhancers	HepG2	liver
6	chr6:30071800-30073000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:30071800-30073400	Weak transcription	HMEC	breast
8	chr6:30071800-30073800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:30071800-30074000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:30071800-30074800	Weak transcription	Spleen	Spleen
11	chr6:30072000-30074000	Weak transcription	Stomach Mucosa	stomach
12	chr6:30072200-30072600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr6:30072200-30072600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
14	chr6:30072200-30073000	Weak transcription	Fetal Intestine Small	intestine
15	chr6:30072200-30078000	Weak transcription	Colonic Mucosa	Colon

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