Variant report

Variant	rs973608
Chromosome Location	chr1:168888946-168888947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:168872513..168874576-chr1:168888387..168891154,2	MCF-7	breast:
2	chr1:168887188..168892256-chr1:169072302..169079040,8	MCF-7	breast:
3	chr1:168875686..168878179-chr1:168887956..168889828,4	MCF-7	breast:
4	chr1:168881969..168885467-chr1:168887830..168890604,3	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction
ENSG00000237707	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10919019	0.87[CEU][hapmap]
rs11577020	0.88[JPT][hapmap]
rs2065128	0.88[JPT][hapmap]
rs2146204	1.00[JPT][hapmap];0.80[TSI][hapmap]
rs55726364	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55982465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56171431	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427156	0.88[JPT][hapmap]
rs7551577	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv437258	chr1:168824111-168890420	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs973608	POGK	cis	cerebellum	SCAN
rs973608	POU2F1	cis	parietal	SCAN
rs973608	SELE	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168879200-168890400	Weak transcription	Aorta	Aorta
2	chr1:168884400-168889800	Weak transcription	Psoas Muscle	Psoas
3	chr1:168886200-168890600	Enhancers	HMEC	breast
4	chr1:168886400-168889000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:168886400-168889400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:168886400-168889600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr1:168886600-168889000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:168886600-168889400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:168886800-168889200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:168886800-168889200	Enhancers	Brain Anterior Caudate	brain
11	chr1:168886800-168890200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:168886800-168890400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:168887000-168889000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:168887200-168891400	Enhancers	Adipose Nuclei	Adipose
15	chr1:168887400-168889200	Weak transcription	Fetal Lung	lung
16	chr1:168887400-168889600	Enhancers	Brain Substantia Nigra	brain
17	chr1:168887600-168889200	Weak transcription	Fetal Stomach	stomach
18	chr1:168887600-168889200	Weak transcription	Left Ventricle	heart
19	chr1:168887600-168889400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:168887800-168889800	Enhancers	HUVEC	blood vessel
21	chr1:168887800-168890400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:168887800-168891800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:168887800-168893400	Enhancers	HepG2	liver
24	chr1:168888000-168889400	Enhancers	A549	lung
25	chr1:168888000-168891800	Enhancers	Stomach Mucosa	stomach
26	chr1:168888200-168889000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:168888200-168889400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:168888200-168889400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:168888400-168889200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:168888400-168889200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:168888400-168889200	Weak transcription	Pancreas	Pancrea
32	chr1:168888400-168889400	Weak transcription	Fetal Kidney	kidney
33	chr1:168888600-168889000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:168888600-168889200	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:168888600-168889400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:168888600-168889600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:168888600-168889600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:168888600-168890400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:168888800-168889200	Weak transcription	Hela-S3	cervix
40	chr1:168888800-168891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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