Variant report

Variant	rs202038
Chromosome Location	chr6:13288648-13288649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13287558-13289732	GM18505	blood:	n/a	n/a
2	POLR2A	chr6:13288389-13289015	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:13288435-13289639	K562	blood:	n/a	n/a
4	PML	chr6:13288493-13288739	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:13286577-13289782	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:13284901-13290945	K562	blood:	n/a	n/a
7	POLR2A	chr6:13288363-13289804	K562	blood:	n/a	n/a
8	POLR2A	chr6:13288385-13289047	GM12878	blood:	n/a	n/a
9	PML	chr6:13287786-13289167	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:13288480-13288833	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:13287591-13289738	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:13287126-13290476	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:13287514-13289720	GM19193	blood:	n/a	n/a
14	POLR2A	chr6:13288387-13289768	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:13287396-13289874	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:13288392-13289741	GM12891	blood:	n/a	n/a
17	MTA3	chr6:13287876-13291052	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:13287490-13289950	GM12892	blood:	n/a	n/a
19	POLR2A	chr6:13288388-13289786	K562	blood:	n/a	n/a
20	POLR2A	chr6:13288298-13288650	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr6:13284889-13290972	GM12891	blood:	n/a	n/a
22	POLR2A	chr6:13288372-13289799	HL-60	blood:	n/a	n/a
23	POLR2A	chr6:13286946-13289896	GM12892	blood:	n/a	n/a
24	POLR2A	chr6:13287500-13289829	GM12891	blood:	n/a	n/a
25	NFATC1	chr6:13287802-13290134	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:13288395-13288727	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:13287681-13289800	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:13288422-13289682	GM15510	blood:	n/a	n/a
29	POLR2A	chr6:13288383-13288875	GM12891	blood:	n/a	n/a
30	POLR2A	chr6:13284835-13292200	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:13288448-13288941	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr6:13288631-13289126	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:13287650-13289766	GM12892	blood:	n/a	n/a
34	NFATC1	chr6:13288425-13288975	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:13287696-13289813	GM12891	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13287477..13291631-chr6:13573758..13576939,3	K562	blood:
2	chr6:13272685..13275870-chr6:13286064..13289898,4	K562	blood:
3	chr6:13287888..13289538-chr6:13307383..13309880,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215022	TF binding region
ENSG00000215022	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000112137	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11759028	0.88[ASN][1000 genomes]
rs1223393	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs12697949	0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs1550526	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs182148	0.90[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2002961	0.80[GIH][hapmap];0.84[JPT][hapmap]
rs202028	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs202030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202034	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202042	0.83[CEU][hapmap];0.80[ASN][1000 genomes]
rs202044	0.83[CEU][hapmap];0.81[ASN][1000 genomes]
rs202045	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs202046	0.81[ASN][1000 genomes]
rs202048	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202053	0.83[CEU][hapmap]
rs202064	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs202068	0.81[EUR][1000 genomes]
rs202069	0.90[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs202070	0.83[CEU][hapmap]
rs202071	0.83[CEU][hapmap]
rs202072	0.83[CEU][hapmap]
rs202073	0.83[CEU][hapmap]
rs35952102	0.91[ASN][1000 genomes]
rs375661	0.80[ASN][1000 genomes]
rs377704	0.83[CEU][hapmap]
rs3800481	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3800482	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs3800483	0.91[ASN][1000 genomes]
rs3800484	0.91[ASN][1000 genomes]
rs3800485	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs3800486	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3823442	0.82[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3823443	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3857594	0.84[JPT][hapmap]
rs405078	0.83[CEU][hapmap];0.80[ASN][1000 genomes]
rs413120	0.83[CEU][hapmap]
rs441213	0.83[CEU][hapmap]
rs445714	0.83[CEU][hapmap];0.80[ASN][1000 genomes]
rs453695	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs454563	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4602719	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs495895	0.80[ASN][1000 genomes]
rs515111	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909879	0.84[JPT][hapmap]
rs6914796	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7742398	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7755309	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs8541	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs878700	0.84[JPT][hapmap]
rs909508	0.84[JPT][hapmap]
rs9296641	0.80[GIH][hapmap];0.84[JPT][hapmap]
rs9296642	0.80[GIH][hapmap];0.84[JPT][hapmap]
rs9369978	0.84[JPT][hapmap]
rs9473908	0.82[JPT][hapmap]
rs9473909	0.84[JPT][hapmap]
rs9473929	0.82[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9473930	0.82[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13270200-13291600	Weak transcription	HSMM	muscle
2	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
3	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
4	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
5	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:13280000-13289000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:13280000-13292600	Weak transcription	NHLF	lung
9	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:13282800-13289400	Strong transcription	Right Ventricle	heart
11	chr6:13282800-13291600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:13283600-13289600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:13284000-13293000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:13284000-13294200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:13285000-13289600	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
17	chr6:13285800-13288800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr6:13285800-13289800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:13285800-13293000	Weak transcription	Brain Angular Gyrus	brain
20	chr6:13285800-13293000	Weak transcription	Brain Substantia Nigra	brain
21	chr6:13286000-13288800	ZNF genes & repeats	Fetal Stomach	stomach
22	chr6:13286400-13288800	ZNF genes & repeats	HepG2	liver
23	chr6:13286400-13289000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:13286600-13288800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr6:13286600-13289000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr6:13286600-13291600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:13286600-13292800	Weak transcription	Colonic Mucosa	Colon
28	chr6:13286800-13288800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr6:13286800-13288800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:13286800-13289400	ZNF genes & repeats	Fetal Intestine Large	intestine
31	chr6:13287000-13288800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:13287000-13288800	ZNF genes & repeats	Lung	lung
33	chr6:13287000-13289200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:13287000-13289600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
35	chr6:13287000-13289800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:13287000-13289800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr6:13287000-13289800	Strong transcription	Gastric	stomach
38	chr6:13287000-13289800	ZNF genes & repeats	Thymus	Thymus
39	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:13287200-13288800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr6:13287200-13288800	ZNF genes & repeats	Fetal Lung	lung
42	chr6:13287200-13290000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:13287200-13292000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:13287200-13292800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:13287400-13288800	Weak transcription	Pancreas	Pancrea
46	chr6:13287400-13294400	Weak transcription	Fetal Kidney	kidney
47	chr6:13287800-13289000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
48	chr6:13287800-13291800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:13287800-13294200	Weak transcription	A549	lung
50	chr6:13287800-13295200	Strong transcription	Monocytes-CD14+_RO01746	blood

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