Variant report

Variant	rs12564929
Chromosome Location	chr1:227955817-227955818
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227948805..227951027-chr1:227953567..227955861,2	MCF-7	breast:
2	chr1:227951099..227952899-chr1:227953091..227955822,2	K562	blood:
3	chr1:227955493..227956067-chr1:228129746..228130568,2	MCF-7	breast:
4	chr1:227955528..227959696-chr1:228132593..228135770,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12563117	1.00[EUR][1000 genomes]
rs12563564	1.00[EUR][1000 genomes]
rs12564736	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564917	1.00[EUR][1000 genomes]
rs12565099	1.00[EUR][1000 genomes]
rs12565109	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12565618	1.00[EUR][1000 genomes]
rs12565653	1.00[EUR][1000 genomes]
rs12566390	1.00[EUR][1000 genomes]
rs12566716	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566948	1.00[ASN][1000 genomes]
rs12567084	1.00[EUR][1000 genomes]
rs12567160	1.00[EUR][1000 genomes]
rs12567934	1.00[EUR][1000 genomes]
rs12568707	1.00[EUR][1000 genomes]
rs1323021	1.00[EUR][1000 genomes]
rs13373816	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841323	1.00[EUR][1000 genomes]
rs16847987	1.00[EUR][1000 genomes]
rs16848026	1.00[EUR][1000 genomes]
rs16848044	1.00[EUR][1000 genomes]
rs16848160	1.00[EUR][1000 genomes]
rs17492440	1.00[EUR][1000 genomes]
rs17492447	1.00[EUR][1000 genomes]
rs2101862	1.00[EUR][1000 genomes]
rs2313220	1.00[EUR][1000 genomes]
rs34984248	1.00[EUR][1000 genomes]
rs35703429	1.00[EUR][1000 genomes]
rs41305134	1.00[ASN][1000 genomes]
rs4462138	1.00[EUR][1000 genomes]
rs60156730	1.00[ASN][1000 genomes]
rs6665512	1.00[EUR][1000 genomes]
rs6684706	1.00[ASN][1000 genomes]
rs73090985	1.00[EUR][1000 genomes]
rs73090986	1.00[EUR][1000 genomes]
rs73090987	1.00[EUR][1000 genomes]
rs73090994	1.00[EUR][1000 genomes]
rs73091000	1.00[EUR][1000 genomes]
rs73092607	1.00[EUR][1000 genomes]
rs73092610	1.00[EUR][1000 genomes]
rs996226	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv3359559	chr1:227953029-227957427	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv3331526	chr1:227953729-227956727	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv3388809	chr1:227953729-227956927	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227946000-227960400	Strong transcription	Fetal Brain Female	brain
2	chr1:227948400-227956000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr1:227949200-227956000	Genic enhancers	Fetal Thymus	thymus
4	chr1:227950800-227963000	Strong transcription	Brain Germinal Matrix	brain
5	chr1:227950800-227974200	Weak transcription	Small Intestine	intestine
6	chr1:227951000-227958600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:227951000-227963200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:227951200-227956600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:227951200-227974400	Weak transcription	Right Atrium	heart
10	chr1:227951400-227963200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:227951600-227961800	Strong transcription	Fetal Stomach	stomach
12	chr1:227951600-227963600	Weak transcription	HUVEC	blood vessel
13	chr1:227951800-227958600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:227951800-227970600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:227952000-227959000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:227952000-227962000	Weak transcription	NHDF-Ad	bronchial
17	chr1:227952200-227960200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:227952200-227962400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:227952600-227958400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:227952800-227956800	Strong transcription	GM12878-XiMat	blood
21	chr1:227952800-227957000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:227952800-227957000	Strong transcription	Aorta	Aorta
23	chr1:227952800-227957800	Genic enhancers	Fetal Muscle Trunk	muscle
24	chr1:227953200-227957000	Genic enhancers	Fetal Intestine Large	intestine
25	chr1:227953200-227959800	Strong transcription	NHLF	lung
26	chr1:227953200-227960400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr1:227953400-227957000	Genic enhancers	Fetal Intestine Small	intestine
28	chr1:227953600-227958800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr1:227953600-227958800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:227953800-227956000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:227953800-227956000	Genic enhancers	Lung	lung
32	chr1:227954000-227956600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:227954000-227957600	Weak transcription	Stomach Mucosa	stomach
34	chr1:227954000-227958000	Genic enhancers	Fetal Muscle Leg	muscle
35	chr1:227954000-227958200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr1:227954000-227958800	Strong transcription	HSMMtube	muscle
37	chr1:227954000-227959800	Strong transcription	Dnd41	blood
38	chr1:227954000-227962600	Strong transcription	Adipose Nuclei	Adipose
39	chr1:227954200-227956000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:227954200-227956600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:227954200-227958000	Strong transcription	A549	lung
42	chr1:227954400-227957200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:227954400-227957800	Strong transcription	NHEK	skin
44	chr1:227954400-227958600	Strong transcription	Brain Substantia Nigra	brain
45	chr1:227954400-227963800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:227954400-227974600	Weak transcription	HMEC	breast
47	chr1:227954600-227956600	Strong transcription	Osteobl	bone
48	chr1:227954600-227957000	Strong transcription	Primary B cells from cord blood	blood
49	chr1:227954600-227957200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr1:227954600-227957400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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