Variant report

Variant	rs12136405
Chromosome Location	chr1:212732289-212732290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212730682..212733368-chr1:212780704..212783808,5	MCF-7	breast:
2	chr1:212730770..212733133-chr1:212778739..212783577,4	MCF-7	breast:
3	chr1:212688702..212690352-chr1:212731451..212733749,2	K562	blood:
4	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
5	chr1:212731186..212732760-chr1:212816538..212818600,2	K562	blood:
6	chr1:212731654..212732474-chr21:44864940..44865899,2	Hela-S3	cervix:
7	chr1:212731550..212733593-chr1:212839647..212842156,2	K562	blood:
8	chr1:212731662..212732424-chr12:46760558..46761178,2	Hela-S3	cervix:
9	chr1:212731890..212732413-chr17:48191672..48192446,2	Hela-S3	cervix:
10	chr1:212650902..212653623-chr1:212731690..212733930,2	K562	blood:
11	chr1:212731680..212733732-chr1:212810239..212812823,2	K562	blood:
12	chr1:212731607..212732508-chr15:59063350..59063852,2	Hela-S3	cervix:
13	chr1:212731711..212732607-chr9:94877004..94877813,2	Hela-S3	cervix:
14	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
15	chr1:211903185..211904905-chr1:212731806..212733794,2	K562	blood:
16	chr1:212676521..212678567-chr1:212731276..212732925,2	K562	blood:
17	chr1:212731878..212732471-chr14:50697417..50697987,2	Hela-S3	cervix:
18	chr1:212731768..212732356-chr6:137539745..137540286,2	Hela-S3	cervix:
19	chr1:212702412..212705298-chr1:212732068..212734031,2	K562	blood:
20	chr1:212731804..212732529-chr7:44121952..44122924,2	Hela-S3	cervix:
21	chr1:212717692..212719261-chr1:212731770..212733992,2	K562	blood:
22	chr1:212717692..212719573-chr1:212732031..212733992,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATF3-1	chr1:212731175-212733073	ENSG00000260805.1

No data

Variant related genes	Relation type
ENSG00000100485	Chromatin interaction
ENSG00000264590	Chromatin interaction
ENSG00000228067	Chromatin interaction
ENSG00000167100	Chromatin interaction
ENSG00000128923	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000090054	Chromatin interaction
ENSG00000122678	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10157292	0.82[ASN][1000 genomes]
rs10863979	0.82[AMR][1000 genomes]
rs10863980	0.84[ASN][1000 genomes]
rs11119963	0.84[AMR][1000 genomes]
rs11119965	0.84[AMR][1000 genomes]
rs11119970	0.83[AMR][1000 genomes]
rs11119971	0.85[AMR][1000 genomes]
rs11119972	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11119973	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119974	0.84[ASN][1000 genomes]
rs11119975	0.83[ASN][1000 genomes]
rs12037048	0.83[ASN][1000 genomes]
rs12038766	0.83[ASN][1000 genomes]
rs12041940	0.85[AMR][1000 genomes]
rs12046640	0.83[ASN][1000 genomes]
rs12729140	0.83[ASN][1000 genomes]
rs3806460	0.84[ASN][1000 genomes]
rs4951453	0.86[AMR][1000 genomes]
rs4951609	0.84[AMR][1000 genomes]
rs4951611	0.84[AMR][1000 genomes]
rs4951613	0.84[ASN][1000 genomes]
rs606996	0.86[AMR][1000 genomes]
rs678640	0.83[AMR][1000 genomes]
rs72649993	0.83[AMR][1000 genomes]
rs7553505	0.85[AMR][1000 genomes]
rs791561	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212731200-212732400	Active TSS	Brain Anterior Caudate	brain
2	chr1:212731200-212732600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:212731200-212732600	Active TSS	Duodenum Mucosa	Duodenum
4	chr1:212731200-212732600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:212731200-212732800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr1:212731200-212732800	Active TSS	Fetal Brain Female	brain
7	chr1:212731400-212732400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:212731400-212732400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:212731400-212732400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:212731400-212732400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:212731400-212732400	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr1:212731400-212732400	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr1:212731400-212732400	Active TSS	HSMMtube	muscle
14	chr1:212731400-212732600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:212731400-212732600	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:212731400-212732600	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr1:212731400-212732600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:212731400-212732600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
19	chr1:212731400-212732600	Active TSS	Brain Hippocampus Middle	brain
20	chr1:212731400-212732600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:212731400-212732600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:212731400-212732600	Active TSS	Fetal Intestine Large	intestine
23	chr1:212731400-212732600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:212731400-212732600	Active TSS	A549	lung
25	chr1:212731400-212732800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:212731400-212732800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:212731600-212732400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:212731600-212732400	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:212731600-212732400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr1:212731600-212732400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:212731600-212732400	Active TSS	Aorta	Aorta
32	chr1:212731600-212732400	Active TSS	Placenta	Placenta
33	chr1:212731600-212732400	Active TSS	Gastric	stomach
34	chr1:212731600-212732400	Active TSS	Left Ventricle	heart
35	chr1:212731600-212732400	Active TSS	Hela-S3	cervix
36	chr1:212731600-212732600	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr1:212731600-212732600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:212731600-212732600	Active TSS	Primary T cells from cord blood	blood
39	chr1:212731600-212732600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:212731600-212732600	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr1:212731600-212732600	Active TSS	Brain Cingulate Gyrus	brain
42	chr1:212731600-212732600	Active TSS	Brain Substantia Nigra	brain
43	chr1:212731600-212732600	Active TSS	Fetal Intestine Small	intestine
44	chr1:212731600-212732600	Active TSS	Fetal Kidney	kidney
45	chr1:212731600-212732600	Transcr. at gene 5' and 3'	Right Atrium	heart
46	chr1:212731600-212732800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:212731600-212732800	Active TSS	Ovary	ovary
48	chr1:212731600-212732800	Flanking Active TSS	HMEC	breast
49	chr1:212731800-212732400	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr1:212731800-212732400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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