Variant report

Variant	rs62411143
Chromosome Location	chr6:80578237-80578238
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	CTCF	chr6:80577802-80578245	IMR90	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
2	RAD21	chr6:80577737-80578305	HCT-116	colon:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
3	CTCF	chr6:80577771-80578255	A549	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
4	CTCF	chr6:80577732-80578360	HCT-116	colon:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
5	CTCF	chr6:80577826-80578257	GM12878	blood:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
6	RAD21	chr6:80577625-80578394	HCT-116	colon:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
7	RAD21	chr6:80577778-80578272	H1-hESC	embryonic stem cell:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
8	RAD21	chr6:80577642-80578338	MCF-7	breast:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
9	ZNF384	chr6:80577857-80578292	GM12878	blood:	n/a	n/a
10	CTCF	chr6:80577612-80578480	A549	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
11	MAX	chr6:80577920-80578521	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr6:80577740-80578306	ECC-1	luminal epithelium:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
13	CTCF	chr6:80577827-80578330	MCF-7	breast:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
14	ZNF384	chr6:80577836-80578304	K562	blood:	n/a	n/a
15	CTCF	chr6:80577913-80578288	Spleen_OC	spleen:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
16	CTCF	chr6:80577732-80578400	HCT-116	colon:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
17	CTCF	chr6:80577816-80578247	K562	blood:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
18	RAD21	chr6:80577744-80578277	A549	lung:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
19	CTCF	chr6:80578200-80578350	HepG2	liver:	n/a	n/a
20	RAD21	chr6:80577887-80578311	MCF-7	breast:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
21	SMC3	chr6:80577360-80578430	SK-N-SH	brain:	n/a	chr6:80578027-80578041 chr6:80578027-80578037
22	RAD21	chr6:80577105-80580479	SK-N-SH	brain:	n/a	chr6:80578023-80578042 chr6:80579004-80579018 chr6:80579461-80579475 chr6:80579484-80579498 chr6:80578027-80578037 chr6:80579477-80579496
23	RAD21	chr6:80577743-80578263	H1-hESC	embryonic stem cell:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
24	SMC3	chr6:80577865-80578252	GM12878	blood:	n/a	chr6:80578027-80578041 chr6:80578027-80578037
25	RAD21	chr6:80577752-80578301	ECC-1	luminal epithelium:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
26	RAD21	chr6:80577790-80578262	H1-hESC	embryonic stem cell:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
27	GATA2	chr6:80577519-80578558	SH-SY5Y	brain:	n/a	n/a
28	MYC	chr6:80577931-80578242	MCF10A-Er-Src	breast:	n/a	n/a
29	CTCF	chr6:80577708-80578334	MCF-7	breast:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
30	RAD21	chr6:80577761-80578291	A549	lung:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
31	CTCF	chr6:80577346-80578651	SK-N-SH	brain:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043

No.	Distal block	Cell Line	Cell type
1	chr6:80423120..80423711-chr6:80577789..80578553,2	K562	blood:
2	chr6:80577908..80579667-chr6:80713971..80715630,2	K562	blood:
3	chr6:80487640..80488609-chr6:80577520..80578268,3	MCF-7	breast:
4	chr6:80487430..80488393-chr6:80577490..80578546,7	K562	blood:
5	chr6:80564754..80565348-chr6:80577673..80578339,2	MCF-7	breast:
6	chr6:80577959..80580872-chr6:80588146..80590140,2	K562	blood:
7	chr6:80571013..80573087-chr6:80576802..80579710,2	K562	blood:

Variant related genes	Relation type
ENSG00000233835	TF binding region
ENSG00000112742	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs103194	0.81[AMR][1000 genomes]
rs1555416	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs168304	0.82[ASN][1000 genomes]
rs182955	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs346287	0.82[ASN][1000 genomes]
rs346289	0.82[ASN][1000 genomes]
rs346293	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs346294	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs346295	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs346296	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346298	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs346300	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346305	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706805	0.92[EUR][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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1021143	chr6:80400195-80598163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	esv3693359	chr6:80539454-80606537	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80576600-80582200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:80577400-80583400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:80577600-80578400	Flanking Active TSS	Brain Anterior Caudate	brain
4	chr6:80577600-80578400	Enhancers	Fetal Intestine Large	intestine
5	chr6:80577600-80579400	Enhancers	Dnd41	blood
6	chr6:80577600-80579800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:80577600-80580000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:80577600-80583200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:80577800-80578400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr6:80577800-80578400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:80577800-80578400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:80577800-80578400	Enhancers	Brain Germinal Matrix	brain
13	chr6:80577800-80578400	Enhancers	Fetal Muscle Leg	muscle
14	chr6:80577800-80578400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr6:80577800-80578400	Enhancers	Stomach Mucosa	stomach
16	chr6:80577800-80578400	Enhancers	K562	blood
17	chr6:80577800-80578600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:80577800-80578600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:80577800-80578600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr6:80577800-80578600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:80577800-80578600	Enhancers	Fetal Thymus	thymus
22	chr6:80577800-80579400	Enhancers	Ovary	ovary
23	chr6:80577800-80580000	Enhancers	Fetal Heart	heart
24	chr6:80577800-80580200	Enhancers	HMEC	breast
25	chr6:80578000-80578400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:80578000-80578400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:80578000-80578400	Enhancers	Fetal Brain Male	brain
28	chr6:80578000-80578400	Enhancers	HUVEC	blood vessel
29	chr6:80578000-80578600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr6:80578000-80579000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:80578000-80579000	Weak transcription	Fetal Stomach	stomach
32	chr6:80578000-80579200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:80578000-80579200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:80578000-80579200	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:80578000-80579200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:80578000-80579200	Weak transcription	Fetal Intestine Small	intestine
37	chr6:80578000-80579200	Weak transcription	Placenta	Placenta
38	chr6:80578000-80579200	Weak transcription	NHDF-Ad	bronchial
39	chr6:80578000-80579400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:80578000-80579400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:80578000-80579400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:80578000-80579400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:80578000-80579400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:80578000-80579400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:80578000-80579400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:80578000-80579400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:80578000-80579400	Weak transcription	Fetal Brain Female	brain
48	chr6:80578000-80579400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:80578000-80579400	Weak transcription	A549	lung
50	chr6:80578000-80579400	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links