Variant report

Variant	rs9349270
Chromosome Location	chr6:44043492-44043493
allele	A/C
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	POLR2A	chr6:44043406-44045001	PFSK-1	brain:	n/a	n/a
2	FOSL2	chr6:44042037-44043660	HepG2	liver:	n/a	chr6:44042993-44043001 chr6:44042992-44043003 chr6:44042992-44043003
3	MAX	chr6:44043448-44043547	GM12878	blood:	n/a	n/a
4	MYBL2	chr6:44040277-44043494	HepG2	liver:	n/a	chr6:44041584-44041599
5	POLR2A	chr6:44040211-44044217	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:44040134-44043640	HepG2	liver:	n/a	n/a
7	RAD21	chr6:44040297-44045355	SK-N-SH	brain:	n/a	chr6:44043089-44043098 chr6:44043985-44043998 chr6:44040377-44040387 chr6:44041243-44041257
8	ELF1	chr6:44041400-44043502	GM12878	blood:	n/a	n/a
9	NFIC	chr6:44042843-44043519	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:44040063-44047982	HepG2	liver:	n/a	n/a
11	HEY1	chr6:44040095-44051472	HepG2	liver:	n/a	chr6:44041314-44041329 chr6:44050861-44050870
12	POLR2A	chr6:44042768-44043635	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:44040073-44047975	HepG2	liver:	n/a	n/a
14	TAF1	chr6:44042099-44043740	HepG2	liver:	n/a	n/a
15	MAX	chr6:44040117-44043655	HepG2	liver:	n/a	chr6:44040351-44040361 chr6:44042834-44042843
16	MAZ	chr6:44038899-44043651	IMR90	lung:	n/a	chr6:44040351-44040361 chr6:44042834-44042843 chr6:44039897-44039906
17	CTCF	chr6:44040684-44043517	SK-N-SH	brain:	n/a	chr6:44043223-44043241
18	MBD4	chr6:44042839-44043508	HepG2	liver:	n/a	n/a
19	JUN	chr6:44043454-44045046	K562	blood:	n/a	n/a
20	ZC3H11A	chr6:44043411-44043559	K562	blood:	n/a	n/a
21	MAX	chr6:44039915-44043593	HepG2	liver:	n/a	chr6:44040351-44040361 chr6:44042834-44042843

No.	Distal block	Cell Line	Cell type
1	chr6:43736197..43742093-chr6:44038080..44048969,27	MCF-7	breast:
2	chr6:43968034..43970803-chr6:44043222..44045394,2	K562	blood:
3	chr6:43736340..43742918-chr6:44039360..44044949,13	MCF-7	breast:
4	chr6:43692540..43694061-chr6:44043360..44045482,2	MCF-7	breast:
5	chr6:43748821..43751206-chr6:44042601..44044445,2	K562	blood:
6	chr6:44042482..44043990-chr6:44221759..44223658,2	K562	blood:
7	chr6:44043421..44045891-chr6:44223702..44225592,2	K562	blood:
8	chr6:44042031..44044413-chr6:44095279..44097168,2	K562	blood:
9	chr6:43877669..43880617-chr6:44042441..44044379,3	K562	blood:
10	chr6:44016213..44019178-chr6:44042475..44044286,2	K562	blood:
11	chr6:44040622..44046991-chr6:44213898..44218144,6	K562	blood:
12	chr6:44042412..44044221-chr6:44084102..44086584,2	K562	blood:
13	chr6:43730164..43744120-chr6:44034600..44052665,50	K562	blood:
14	chr6:44042539..44044412-chr6:44091796..44094551,2	K562	blood:
15	chr6:44040972..44043900-chr6:44213898..44215544,2	K562	blood:
16	chr6:43736916..43737842-chr6:44043254..44044419,3	K562	blood:
17	chr6:43736441..43745894-chr6:44037513..44049664,39	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM63B-3	chr6:44043143-44043750	NONHSAT112943

Variant related genes	Relation type
ENSG00000237686	TF binding region
ENSG00000112715	Chromatin interaction
ENSG00000265700	Chromatin interaction
ENSG00000272114	Chromatin interaction
ENSG00000181577	Chromatin interaction
ENSG00000137216	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000157593	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10948121	1.00[AFR][1000 genomes]
rs12191873	1.00[AFR][1000 genomes]
rs12202501	1.00[AFR][1000 genomes]
rs12206795	1.00[AFR][1000 genomes]
rs13210320	0.93[EUR][1000 genomes]
rs2064639	1.00[AFR][1000 genomes]
rs2064640	1.00[AFR][1000 genomes]
rs2092870	1.00[AFR][1000 genomes]
rs2236061	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734697	1.00[AFR][1000 genomes]
rs4628095	1.00[AFR][1000 genomes]
rs4711764	1.00[AFR][1000 genomes]
rs4711766	1.00[AFR][1000 genomes]
rs4714738	1.00[AFR][1000 genomes]
rs4714750	1.00[AFR][1000 genomes]
rs4714754	1.00[AFR][1000 genomes]
rs4714759	1.00[AFR][1000 genomes]
rs62401766	1.00[AFR][1000 genomes]
rs62403186	0.96[EUR][1000 genomes]
rs62403189	1.00[AFR][1000 genomes]
rs9349271	1.00[AFR][1000 genomes]
rs9349272	1.00[AFR][1000 genomes]
rs9349275	1.00[AFR][1000 genomes]
rs9357432	1.00[AFR][1000 genomes]
rs9369448	1.00[AFR][1000 genomes]
rs9369449	1.00[AFR][1000 genomes]
rs9369450	1.00[AFR][1000 genomes]
rs9369453	1.00[AFR][1000 genomes]
rs9369454	1.00[AFR][1000 genomes]
rs9369457	1.00[AFR][1000 genomes]
rs9381286	0.92[EUR][1000 genomes]
rs9381287	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9381294	1.00[AFR][1000 genomes]
rs9394984	1.00[AFR][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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44039000-44043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:44040200-44045400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:44041000-44044600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr6:44041200-44045400	Enhancers	HMEC	breast
5	chr6:44041400-44043600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:44041600-44045000	Enhancers	Pancreas	Pancrea
7	chr6:44041600-44045200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:44041800-44044600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:44041800-44044600	Enhancers	Fetal Intestine Small	intestine
10	chr6:44041800-44045600	Enhancers	Fetal Intestine Large	intestine
11	chr6:44042000-44043800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:44042000-44044600	Enhancers	Fetal Stomach	stomach
13	chr6:44042200-44044000	Weak transcription	Small Intestine	intestine
14	chr6:44042200-44047000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:44042400-44043600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:44042400-44043800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:44042400-44043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:44042400-44043800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:44042400-44043800	Enhancers	A549	lung
20	chr6:44042400-44044000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr6:44042400-44044000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:44042400-44044000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:44042400-44044000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:44042400-44044000	Weak transcription	Liver	Liver
25	chr6:44042400-44044000	Enhancers	Fetal Brain Male	brain
26	chr6:44042400-44044000	Enhancers	Fetal Thymus	thymus
27	chr6:44042400-44044000	Weak transcription	Psoas Muscle	Psoas
28	chr6:44042400-44044200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:44042400-44044200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:44042400-44044200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:44042400-44044200	Enhancers	Fetal Brain Female	brain
32	chr6:44042400-44044200	Enhancers	Right Ventricle	heart
33	chr6:44042400-44044200	Enhancers	NHDF-Ad	bronchial
34	chr6:44042400-44044400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:44042400-44044800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:44042400-44044800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr6:44042400-44045000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:44042400-44045000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:44042400-44045000	Enhancers	Left Ventricle	heart
40	chr6:44042400-44045400	Enhancers	Brain Hippocampus Middle	brain
41	chr6:44042400-44045800	Enhancers	Fetal Lung	lung
42	chr6:44042400-44047400	Enhancers	Fetal Heart	heart
43	chr6:44042600-44044000	Enhancers	Brain Germinal Matrix	brain
44	chr6:44042600-44044600	Weak transcription	Ovary	ovary
45	chr6:44042600-44044800	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr6:44042600-44045000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:44042600-44045000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:44042600-44045000	Bivalent Enhancer	Placenta	Placenta
49	chr6:44042800-44043800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:44042800-44043800	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links