Variant report

Variant	rs2281919
Chromosome Location	chr6:33663171-33663172
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:33661582-33663177	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:33662575-33664313	K562	blood:	n/a	n/a
3	POLR2A	chr6:33662091-33663836	K562	blood:	n/a	n/a
4	POLR2A	chr6:33662990-33663318	K562	blood:	n/a	n/a
5	POLR2A	chr6:33662740-33663836	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr6:33660657-33663799	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:33662805-33663866	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr6:33662026-33666005	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:33662069-33664724	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:33662113-33666054	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:33660869-33664890	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:33663102-33663633	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr6:33662776-33663807	HL-60	blood:	n/a	n/a
14	POLR2A	chr6:33662019-33665616	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr6:33657437-33666414	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:33662092-33663172	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:33662094-33663781	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr6:33662182-33664245	K562	blood:	n/a	n/a
19	POLR2A	chr6:33661275-33663273	MCF-7	breast:	n/a	n/a
20	POLR2A	chr6:33658911-33667009	K562	blood:	n/a	n/a
21	POLR2A	chr6:33662747-33663658	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr6:33662086-33663570	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr6:33662932-33663482	U87	brain:	n/a	n/a
24	POLR2A	chr6:33662149-33663255	PBDE	blood:	n/a	n/a
25	POLR2A	chr6:33662770-33663199	A549	lung:	n/a	n/a
26	POLR2A	chr6:33662639-33664943	HCT-116	colon:	n/a	n/a
27	POLR2A	chr6:33662717-33663787	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:33658928-33664260	K562	blood:	n/a	n/a
29	POLR2A	chr6:33657421-33665985	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
2	chr6:33377496..33379251-chr6:33661661..33664420,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3934	TF binding region
ENSG00000112511	Chromatin interaction
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10456075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947415	0.84[CEU][hapmap]
rs10947427	0.83[GIH][hapmap]
rs10947432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12189725	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs12190155	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195707	0.84[CEU][hapmap]
rs12199132	0.85[ASN][1000 genomes]
rs12203688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12205398	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12207382	0.85[JPT][hapmap]
rs12211490	1.00[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs12211554	0.85[JPT][hapmap]
rs12661400	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13200063	0.85[JPT][hapmap]
rs13204162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13204975	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207666	0.85[ASN][1000 genomes]
rs13214874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274459	0.85[JPT][hapmap];0.87[TSI][hapmap]
rs2281831	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2281917	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281918	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296737	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34139049	0.82[ASN][1000 genomes]
rs34778247	1.00[EUR][1000 genomes]
rs35095444	0.92[EUR][1000 genomes]
rs35274562	0.82[ASN][1000 genomes]
rs35646598	0.82[ASN][1000 genomes]
rs35698850	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3793080	0.80[TSI][hapmap]
rs3806107	0.80[TSI][hapmap]
rs3818526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818532	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6925337	0.85[JPT][hapmap]
rs729376	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs877187	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs9296097	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9469554	0.92[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2281919	LEMD2	cis	parietal	SCAN
rs2281919	LEMD2	cis	cerebellum	SCAN
rs2281919	C6orf125	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:33655000-33663600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:33655600-33664800	Weak transcription	Aorta	Aorta
12	chr6:33656400-33666000	Genic enhancers	Spleen	Spleen
13	chr6:33658000-33663400	Genic enhancers	Right Ventricle	heart
14	chr6:33658000-33667200	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr6:33658200-33666600	Genic enhancers	Fetal Muscle Leg	muscle
16	chr6:33658600-33663400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:33658600-33666400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:33659000-33666600	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr6:33659200-33665200	Genic enhancers	HMEC	breast
20	chr6:33659200-33665400	Genic enhancers	NHDF-Ad	bronchial
21	chr6:33659200-33665800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:33659200-33666600	Enhancers	Right Atrium	heart
23	chr6:33659400-33663600	Enhancers	Psoas Muscle	Psoas
24	chr6:33659400-33663800	Enhancers	HSMMtube	muscle
25	chr6:33659400-33664200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr6:33659400-33665000	Genic enhancers	Duodenum Mucosa	Duodenum
27	chr6:33659400-33666400	Genic enhancers	Fetal Thymus	thymus
28	chr6:33659400-33668400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr6:33659600-33663600	Enhancers	NH-A	brain
30	chr6:33659600-33664600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:33659600-33665600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:33659600-33666400	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:33659600-33667000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:33659800-33663200	Genic enhancers	Osteobl	bone
35	chr6:33659800-33664800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:33659800-33665600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:33659800-33666000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr6:33659800-33666600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:33659800-33666600	Genic enhancers	Fetal Stomach	stomach
40	chr6:33660000-33664600	Enhancers	Primary B cells from cord blood	blood
41	chr6:33660000-33666200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr6:33660200-33663800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:33660200-33665600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:33660200-33667200	Genic enhancers	Lung	lung
45	chr6:33660200-33667800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:33660200-33669400	Strong transcription	HepG2	liver
47	chr6:33660400-33664600	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr6:33660400-33664600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:33660400-33665600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:33660400-33665800	Enhancers	HUVEC	blood vessel

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