Variant report

Variant	rs1340867
Chromosome Location	chr1:225611845-225611846
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	JUN	chr1:225611820-225617257	K562	blood:	n/a	chr1:225613227-225613237 chr1:225616567-225616575 chr1:225615250-225615261 chr1:225616568-225616575 chr1:225612971-225612983 chr1:225616565-225616577 chr1:225613226-225613238 chr1:225613227-225613237 chr1:225613228-225613236 chr1:225616567-225616575 chr1:225615989-225615998 chr1:225612930-225612939 chr1:225613227-225613237 chr1:225616648-225616657 chr1:225615862-225615871 chr1:225616566-225616576
2	EP300	chr1:225609718-225612078	SK-N-SH	brain:	n/a	chr1:225609737-225609751
3	MXI1	chr1:225609788-225616921	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:225609832..225612207-chr1:225614120..225615659,2	MCF-7	breast:
2	chr1:225611374..225613907-chr1:225615245..225617904,3	MCF-7	breast:
3	chr1:225611259..225613937-chr1:225629471..225632737,4	K562	blood:

Variant related genes	Relation type
LBR	TF binding region
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1056607	0.88[ASW][hapmap];0.85[CHD][hapmap];0.85[YRI][hapmap]
rs10799312	0.81[CHB][hapmap]
rs11588279	0.92[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1340865	0.82[CHB][hapmap]
rs2066233	0.88[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2185529	0.99[ASN][1000 genomes]
rs3766930	0.82[CHB][hapmap]
rs499782	0.81[CHB][hapmap]
rs6426075	0.82[CHB][hapmap]
rs6684787	0.90[ASN][1000 genomes]
rs6687980	0.89[ASN][1000 genomes]
rs6696038	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7541888	0.89[ASN][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1340867	C1orf95	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225599800-225614000	Weak transcription	Right Ventricle	heart
2	chr1:225602800-225612400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:225602800-225613600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:225603400-225612400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:225607000-225612200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:225607000-225612400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:225607000-225612400	Weak transcription	Brain Angular Gyrus	brain
8	chr1:225607000-225612400	Weak transcription	Esophagus	oesophagus
9	chr1:225607000-225613800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:225607200-225612000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:225607200-225612000	Weak transcription	HSMMtube	muscle
12	chr1:225607200-225612400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:225607200-225612400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:225607200-225612400	Weak transcription	Ovary	ovary
15	chr1:225607400-225612200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:225607400-225612400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:225607600-225612200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:225607600-225612400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:225607600-225612400	Weak transcription	Placenta	Placenta
20	chr1:225608200-225612400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:225608400-225612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:225608400-225612600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:225609600-225615200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:225609800-225612000	Enhancers	Fetal Brain Female	brain
25	chr1:225609800-225612200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr1:225609800-225613200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:225609800-225613800	Enhancers	Fetal Brain Male	brain
28	chr1:225609800-225614200	Enhancers	Small Intestine	intestine
29	chr1:225610000-225612000	Enhancers	Primary hematopoietic stem cells	blood
30	chr1:225610000-225612000	Genic enhancers	K562	blood
31	chr1:225610000-225612400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:225610000-225612400	Weak transcription	Right Atrium	heart
33	chr1:225610000-225612600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:225610000-225612600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:225610000-225613000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:225610000-225613600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:225610000-225613800	Enhancers	Fetal Lung	lung
38	chr1:225610200-225612000	Enhancers	Brain Germinal Matrix	brain
39	chr1:225610200-225612600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:225610200-225613400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr1:225610200-225613600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:225610200-225613800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:225610400-225612000	Genic enhancers	Primary B cells from cord blood	blood
44	chr1:225610400-225612200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr1:225610400-225612200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr1:225610400-225612200	Enhancers	A549	lung
47	chr1:225610400-225612200	Enhancers	Osteobl	bone
48	chr1:225610400-225612400	Genic enhancers	Hela-S3	cervix
49	chr1:225610400-225612600	Enhancers	NHLF	lung
50	chr1:225610400-225612800	Genic enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links