Variant report

Variant	rs6672415
Chromosome Location	chr1:180881148-180881149
allele	C/T
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	RAD21	chr1:180880914-180881462	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr1:180881090-180881502	H1-hESC	embryonic stem cell:	n/a	n/a
3	RELA	chr1:180880720-180881647	GM18951	blood:	n/a	chr1:180881341-180881350 chr1:180881341-180881350
4	POLR2A	chr1:180880996-180881179	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr1:180880896-180881958	H1-hESC	embryonic stem cell:	n/a	chr1:180881432-180881442 chr1:180881328-180881338 chr1:180881768-180881775 chr1:180881768-180881775 chr1:180881434-180881443 chr1:180881768-180881775
6	POLR2A	chr1:180880961-180882409	GM15510	blood:	n/a	n/a
7	YY1	chr1:180880655-180881162	H1-hESC	embryonic stem cell:	n/a	chr1:180881063-180881074 chr1:180880826-180880838
8	BACH1	chr1:180881122-180882154	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:180881034-180881188	Gliobla	brain:	n/a	n/a
10	POLR2A	chr1:180880900-180882751	GM18526	blood:	n/a	n/a
11	RCOR1	chr1:180881067-180881245	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:180880908-180882687	GM18951	blood:	n/a	n/a
13	SIN3A	chr1:180880808-180882632	H1-hESC	embryonic stem cell:	n/a	chr1:180881456-180881467 chr1:180882205-180882218 chr1:180882202-180882211 chr1:180881883-180881896 chr1:180882153-180882166
14	CTCF	chr1:180881120-180881270	HA-sp	spinal cord:	n/a	n/a
15	CTBP2	chr1:180880845-180882924	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:180881041-180882440	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:180880753-180882509	GM19193	blood:	n/a	n/a
18	POLR2A	chr1:180880810-180882658	GM19099	blood:	n/a	n/a
19	MAZ	chr1:180880823-180883145	IMR90	lung:	n/a	chr1:180882510-180882520 chr1:180881689-180881699
20	POLR2A	chr1:180880603-180882704	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD2	chr1:180880927-180881273	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:180881051-180881244	ProgFib	skin:	n/a	n/a
23	POLR2A	chr1:180880850-180882738	H1-hESC	embryonic stem cell:	n/a	n/a
24	TBP	chr1:180880930-180881898	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr1:180880906-180881685	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180874718..180876670-chr1:180880822..180883224,2	K562	blood:
2	chr1:180879805..180882226-chr1:180894957..180896873,2	MCF-7	breast:

Variant related genes	Relation type
KIAA1614	TF binding region
ENSG00000225857	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10753226	0.87[AMR][1000 genomes]
rs11800333	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs11812056	0.93[ASN][1000 genomes]
rs35070801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536392	0.86[CHB][hapmap];0.87[MEX][hapmap];0.87[AMR][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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3436549	chr1:180880954-180883502	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6672415	C1orf220	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180877600-180881200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:180879200-180881800	Weak transcription	A549	lung
3	chr1:180880000-180881200	Bivalent Enhancer	Fetal Thymus	thymus
4	chr1:180880400-180881200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:180880400-180881200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr1:180880600-180881200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:180880600-180881200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:180880600-180881200	Flanking Active TSS	Osteobl	bone
9	chr1:180880600-180881400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:180880800-180881200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
11	chr1:180880800-180881200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
12	chr1:180880800-180881200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr1:180880800-180881200	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr1:180880800-180881200	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr1:180880800-180881200	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr1:180880800-180881200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr1:180880800-180881200	Flanking Active TSS	Colon Smooth Muscle	Colon
18	chr1:180880800-180881200	Flanking Active TSS	Fetal Brain Male	brain
19	chr1:180880800-180881200	Flanking Active TSS	Fetal Stomach	stomach
20	chr1:180880800-180881200	Flanking Active TSS	Right Ventricle	heart
21	chr1:180880800-180881200	Flanking Active TSS	HSMMtube	muscle
22	chr1:180880800-180881200	Bivalent/Poised TSS	NHEK	skin
23	chr1:180880800-180881400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
24	chr1:180880800-180881400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:180880800-180881400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
26	chr1:180880800-180881400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
27	chr1:180880800-180881400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:180880800-180881400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:180880800-180881400	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr1:180880800-180881400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
31	chr1:180880800-180881400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr1:180880800-180881400	Bivalent Enhancer	Small Intestine	intestine
33	chr1:180880800-180881400	Enhancers	Spleen	Spleen
34	chr1:180880800-180881400	Flanking Active TSS	NH-A	brain
35	chr1:180880800-180881400	Flanking Active TSS	NHLF	lung
36	chr1:180880800-180881600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:180880800-180881600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr1:180880800-180881600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
39	chr1:180880800-180881600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr1:180880800-180881600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr1:180880800-180881800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:180880800-180881800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr1:180880800-180882200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr1:180880800-180882400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr1:180880800-180882400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr1:180880800-180882800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:180880800-180882800	Active TSS	Brain Angular Gyrus	brain
48	chr1:180880800-180882800	Active TSS	Fetal Brain Female	brain
49	chr1:180880800-180883000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr1:180880800-180883000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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