Variant report

Variant	rs36030243
Chromosome Location	chr17:38460861-38460862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr17:38460587-38461021	IMR90	lung:	n/a	chr17:38460746-38460762 chr17:38460745-38460759 chr17:38460746-38460757
2	POLR2A	chr17:38459387-38460934	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:38459274-38461086	HL-60	blood:	n/a	n/a
4	POLR2A	chr17:38460662-38462109	HepG2	liver:	n/a	n/a
5	EP300	chr17:38460574-38461008	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr17:38459226-38462021	GM12892	blood:	n/a	n/a
7	NFIC	chr17:38459191-38461165	SK-N-SH	brain:	n/a	chr17:38460289-38460305 chr17:38460288-38460305
8	POLR2A	chr17:38460651-38461028	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr17:38458825-38461385	SK-N-SH	brain:	n/a	chr17:38459432-38459442 chr17:38459430-38459443 chr17:38459432-38459444 chr17:38459427-38459446 chr17:38459431-38459440
10	POLR2A	chr17:38460709-38461005	GM12891	blood:	n/a	n/a
11	POLR2A	chr17:38458942-38461260	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr17:38460515-38461044	U87	brain:	n/a	n/a
13	POLR2A	chr17:38460479-38461467	K562	blood:	n/a	n/a
14	POLR2A	chr17:38459735-38461047	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr17:38459270-38460975	GM12892	blood:	n/a	n/a
16	TCF12	chr17:38459160-38461267	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr17:38460612-38460905	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr17:38460445-38461029	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr17:38459425-38460914	SK-N-MC	brain:	n/a	n/a
20	EP300	chr17:38458817-38461269	SK-N-SH	brain:	n/a	chr17:38459874-38459887
21	POLR2A	chr17:38459179-38462046	GM12892	blood:	n/a	n/a
22	POLR2A	chr17:38459064-38462073	K562	blood:	n/a	n/a
23	POLR2A	chr17:38459129-38461039	K562	blood:	n/a	n/a
24	GATA3	chr17:38459194-38461150	SK-N-SH	brain:	n/a	chr17:38460805-38460822 chr17:38460340-38460351
25	POLR2A	chr17:38459927-38460999	U87	brain:	n/a	n/a
26	GATA3	chr17:38460703-38460907	SH-SY5Y	brain:	n/a	chr17:38460805-38460822
27	TCF12	chr17:38459181-38461236	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr17:38458775-38462061	PFSK-1	brain:	n/a	n/a
29	RAD21	chr17:38460491-38461057	IMR90	lung:	n/a	n/a
30	POLR2A	chr17:38459161-38462037	GM12892	blood:	n/a	n/a
31	SMC3	chr17:38458798-38461207	SK-N-SH	brain:	n/a	chr17:38459428-38459442
32	POLR2A	chr17:38459226-38461005	U87	brain:	n/a	n/a
33	CTCF	chr17:38458833-38461008	A549	lung:	n/a	chr17:38459427-38459443 chr17:38459426-38459444 chr17:38459428-38459449 chr17:38459431-38459441
34	CTCF	chr17:38458940-38460875	SK-N-SH	brain:	n/a	chr17:38459427-38459443 chr17:38459426-38459444 chr17:38459428-38459449 chr17:38459431-38459441
35	POLR2A	chr17:38459191-38462034	GM12891	blood:	n/a	n/a
36	POLR2A	chr17:38459266-38460987	HepG2	liver:	n/a	n/a
37	POLR2A	chr17:38460013-38461033	K562	blood:	n/a	n/a
38	POLR2A	chr17:38460798-38461458	HL-60	blood:	n/a	n/a
39	POLR2A	chr17:38460541-38460983	GM12891	blood:	n/a	n/a
40	POLR2A	chr17:38460441-38461500	H1-hESC	embryonic stem cell:	n/a	n/a
41	EP300	chr17:38459647-38461227	SK-N-SH	brain:	n/a	chr17:38459874-38459887
42	POLR2A	chr17:38459295-38461002	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr17:38458998-38461101	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38458898..38461237-chr17:38499745..38502287,2	K562	blood:
2	chr17:38267756..38269556-chr17:38459898..38462579,2	K562	blood:
3	chr17:38457066..38460899-chr17:38504442..38513119,13	K562	blood:
4	chr17:38331368..38338782-chr17:38460574..38470405,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDC6-1	chr17:38459457-38460909	ENSG00000270145.1

Variant related genes	Relation type
RARA	TF binding region
ENSG00000131759	Chromatin interaction
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11078940	0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs12051734	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12103711	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12946680	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13706	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16965687	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs1807273	0.92[ASN][1000 genomes]
rs2077464	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2120200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280400	0.87[GIH][hapmap]
rs28537537	0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs35286757	0.88[ASN][1000 genomes]
rs4077125	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs4134994	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4566234	0.81[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs55656553	0.96[ASN][1000 genomes]
rs57179137	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59406133	0.86[ASN][1000 genomes]
rs6503539	0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap]
rs7217852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs7359537	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs8066144	0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs9303285	0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs9303286	0.80[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9892946	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9893520	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9894625	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9896312	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9904021	0.81[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs9904270	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[ASN][1000 genomes]
rs9908034	0.84[CHB][hapmap]
rs9916460	0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs9916782	0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]

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	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38444800-38462600	Weak transcription	Esophagus	oesophagus
2	chr17:38445600-38462600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:38446000-38461000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:38450800-38461200	Strong transcription	Dnd41	blood
5	chr17:38452600-38461000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr17:38452800-38461400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:38452800-38461400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr17:38453000-38461000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:38453000-38462600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:38453400-38461200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr17:38455800-38462800	Weak transcription	Ovary	ovary
12	chr17:38459000-38461200	Genic enhancers	HMEC	breast
13	chr17:38459000-38461800	Enhancers	NHLF	lung
14	chr17:38459000-38462400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr17:38459000-38465400	Enhancers	Fetal Muscle Leg	muscle
16	chr17:38459000-38465400	Enhancers	Fetal Stomach	stomach
17	chr17:38459200-38461000	Genic enhancers	NHEK	skin
18	chr17:38459200-38461400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr17:38459200-38461600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:38459200-38462800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:38459200-38465200	Enhancers	Fetal Intestine Large	intestine
22	chr17:38459200-38465400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr17:38459200-38473800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr17:38459400-38461000	Genic enhancers	Fetal Thymus	thymus
25	chr17:38459400-38461200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr17:38459400-38461400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:38459400-38461400	Enhancers	Adipose Nuclei	Adipose
28	chr17:38459400-38461400	Enhancers	NH-A	brain
29	chr17:38459600-38461000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
30	chr17:38459600-38461200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr17:38459600-38461400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:38459600-38461400	Enhancers	Brain Germinal Matrix	brain
33	chr17:38459600-38461800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr17:38459600-38462200	Enhancers	Fetal Muscle Trunk	muscle
35	chr17:38459600-38465200	Enhancers	Placenta	Placenta
36	chr17:38459800-38461000	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr17:38459800-38462600	Weak transcription	Stomach Mucosa	stomach
38	chr17:38459800-38462800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr17:38459800-38462800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr17:38460000-38461400	Enhancers	Rectal Smooth Muscle	rectum
41	chr17:38460000-38461800	Weak transcription	Fetal Intestine Small	intestine
42	chr17:38460000-38462600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr17:38460000-38462600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr17:38460000-38462600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr17:38460000-38463200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr17:38460000-38463400	Weak transcription	Primary B cells from cord blood	blood
47	chr17:38460000-38463400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:38460000-38464000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr17:38460000-38465200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:38460000-38465200	Weak transcription	Brain Angular Gyrus	brain

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