Variant report

Variant	rs2378605
Chromosome Location	chr1:222905553-222905554
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	SPI1	chr1:222905502-222906564	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:222903061..222906821-chr1:222906976..222911294,5	K562	blood:
2	chr1:222903370..222905745-chr1:222909291..222910928,2	MCF-7	breast:
3	chr1:222885857..222889762-chr1:222903020..222907043,5	K562	blood:
4	chr1:222892763..222894446-chr1:222903133..222906002,2	K562	blood:

Variant related genes	Relation type
FAM177B	TF binding region
ENSG00000162819	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000197520	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17531007	1.00[CHB][hapmap]
rs17531580	1.00[CHB][hapmap]
rs17532757	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002145	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3008621	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3008630	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4240934	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61824333	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs904323	1.00[CHB][hapmap]

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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2378605	C1orf58	cis	parietal	SCAN
rs2378605	HOMER2	trans	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222887200-222909600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:222887400-222908800	Weak transcription	Stomach Mucosa	stomach
3	chr1:222887400-222909600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:222887400-222912000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:222887600-222912400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:222888000-222909200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:222888200-222909200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:222888200-222909600	Weak transcription	Spleen	Spleen
9	chr1:222888200-222910200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:222888200-222910400	Strong transcription	Fetal Thymus	thymus
11	chr1:222888400-222905600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:222888400-222907800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:222888400-222908200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:222888400-222908600	Strong transcription	HSMM	muscle
15	chr1:222888400-222908600	Strong transcription	NHDF-Ad	bronchial
16	chr1:222888400-222909600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:222888400-222909600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:222888400-222910000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:222888400-222910000	Strong transcription	Fetal Intestine Large	intestine
20	chr1:222888400-222910200	Strong transcription	Placenta	Placenta
21	chr1:222888400-222910800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:222888600-222908400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:222888600-222909800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:222888600-222910400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr1:222888600-222910800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:222888600-222911200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:222888600-222911400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:222888800-222908800	Strong transcription	Dnd41	blood
29	chr1:222889000-222908200	Strong transcription	NH-A	brain
30	chr1:222889000-222910000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr1:222889000-222910200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:222889000-222911200	Strong transcription	Liver	Liver
33	chr1:222889000-222911400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:222889200-222910000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:222889200-222910600	Strong transcription	Adipose Nuclei	Adipose
36	chr1:222889600-222906000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:222889600-222908200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:222889600-222909400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:222889800-222909200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:222889800-222909600	Strong transcription	HUVEC	blood vessel
41	chr1:222889800-222910200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:222890000-222910000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:222891400-222908800	Strong transcription	Brain Anterior Caudate	brain
44	chr1:222891600-222909800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:222891800-222905600	Strong transcription	Colon Smooth Muscle	Colon
46	chr1:222891800-222910200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:222892000-222909000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:222892000-222910200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:222892000-222911000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:222892200-222907800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links