Variant report

Variant	rs12068175
Chromosome Location	chr1:153756191-153756192
allele	C/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:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153752661..153757715-chr1:153961416..153965311,5	K562	blood:
2	chr1:153753973..153757934-chr1:153914747..153920506,6	MCF-7	breast:
3	chr1:153755492..153756298-chr17:79868575..79869130,2	Hela-S3	cervix:
4	chr1:153754789..153757770-chr1:153948823..153951107,2	MCF-7	breast:
5	chr1:153718689..153722494-chr1:153754565..153757255,3	MCF-7	breast:
6	chr1:153754951..153758760-chr1:153962914..153965796,4	K562	blood:
7	chr1:153754842..153757313-chr1:153895286..153897128,2	K562	blood:
8	chr1:153754842..153757396-chr1:153894711..153897128,3	K562	blood:
9	chr1:153756176..153757958-chr1:153963076..153964678,2	MCF-7	breast:
10	chr1:153754517..153758077-chr1:153759140..153763614,7	K562	blood:
11	chr1:153643199..153644898-chr1:153754858..153757761,2	K562	blood:
12	chr1:153755790..153756651-chr17:56708942..56709615,2	HCT-116	colon:
13	chr1:153754741..153757518-chr1:153930305..153932250,2	K562	blood:
14	chr1:153755801..153756363-chr3:23986450..23987372,2	Hela-S3	cervix:
15	chr1:153755974..153756578-chr12:120729272..120729909,2	Hela-S3	cervix:
16	chr1:153754759..153758039-chr1:153961384..153964701,3	MCF-7	breast:
17	chr1:153755524..153756377-chr3:49058577..49059432,2	Hela-S3	cervix:
18	chr1:153754814..153757464-chr1:153760573..153762227,2	MCF-7	breast:
19	chr1:153631452..153634025-chr1:153753430..153756268,2	MCF-7	breast:
20	chr1:153755717..153756474-chr9:140172008..140172597,2	Hela-S3	cervix:
21	chr1:153754359..153756426-chr1:153773567..153776209,2	MCF-7	breast:
22	chr1:153754545..153757490-chr1:153768363..153770074,2	MCF-7	breast:
23	chr1:153756165..153756717-chr15:72523037..72523938,2	Hela-S3	cervix:
24	chr1:153752949..153756283-chr1:153940484..153942451,4	MCF-7	breast:
25	chr1:153755894..153756700-chr9:103188516..103189454,2	Hela-S3	cervix:
26	chr1:152019890..152020563-chr1:153755779..153756680,2	Hela-S3	cervix:
27	chr1:153753211..153758068-chr1:153759455..153763614,7	K562	blood:
28	chr1:153756018..153757611-chr1:153930305..153933106,2	K562	blood:
29	chr1:153754805..153756401-chr1:153959056..153960876,2	K562	blood:
30	chr1:153755923..153756434-chr6:26124092..26124959,2	Hela-S3	cervix:
31	chr1:153755773..153757847-chr1:153948754..153951172,2	K562	blood:
32	chr1:153755765..153756406-chr1:154155175..154155686,2	Hela-S3	cervix:
33	chr1:153649322..153651332-chr1:153754891..153757432,2	MCF-7	breast:
34	chr1:153752474..153754090-chr1:153754939..153756704,2	K562	blood:
35	chr1:153755771..153756341-chr12:7037095..7037808,2	Hela-S3	cervix:
36	chr1:153754767..153757763-chr1:153916863..153919797,5	MCF-7	breast:
37	chr1:153755388..153757822-chr1:153776509..153778942,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000180596	Chromatin interaction
ENSG00000160741	Chromatin interaction
ENSG00000143543	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000185813	Chromatin interaction
ENSG00000143614	Chromatin interaction
ENSG00000198113	Chromatin interaction
ENSG00000111676	Chromatin interaction
ENSG00000066697	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000169418	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000272654	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1127092	0.84[ASN][1000 genomes]
rs12033532	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12043354	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2072704	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2297895	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs35036680	0.86[ASN][1000 genomes]
rs6427298	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
9	nsv515962	chr1:153752139-153773429	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12068175	HAX1	cis	parietal	SCAN
rs12068175	HAX1	cis	cerebellum	SCAN
rs12068175	HAX1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153755400-153756400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:153755400-153756400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:153755400-153756400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:153755400-153756400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:153755400-153756400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:153755400-153756400	Active TSS	Brain Hippocampus Middle	brain
7	chr1:153755400-153756400	Active TSS	A549	lung
8	chr1:153755400-153756600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:153755400-153756600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:153755400-153756600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:153755400-153756600	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr1:153755400-153756600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr1:153755400-153756600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr1:153755400-153756600	Active TSS	Right Atrium	heart
15	chr1:153755400-153756600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr1:153755600-153756200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:153755600-153756200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:153755600-153756200	Active TSS	Ovary	ovary
19	chr1:153755600-153756200	Active TSS	Placenta Amnion	Placenta Amnion
20	chr1:153755600-153756400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:153755600-153756400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:153755600-153756400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:153755600-153756400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:153755600-153756400	Active TSS	Brain Angular Gyrus	brain
25	chr1:153755600-153756400	Active TSS	Brain Cingulate Gyrus	brain
26	chr1:153755600-153756400	Active TSS	Left Ventricle	heart
27	chr1:153755600-153756400	Active TSS	Rectal Smooth Muscle	rectum
28	chr1:153755600-153756400	Active TSS	NHLF	lung
29	chr1:153755600-153756600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr1:153755600-153756600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:153755600-153756600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:153755600-153756600	Active TSS	Aorta	Aorta
33	chr1:153755600-153756600	Active TSS	Colonic Mucosa	Colon
34	chr1:153755600-153756600	Active TSS	Pancreas	Pancrea
35	chr1:153755600-153756600	Active TSS	Psoas Muscle	Psoas
36	chr1:153755600-153756600	Active TSS	Right Ventricle	heart
37	chr1:153755600-153756600	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr1:153755600-153756600	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:153755600-153756600	Active TSS	HSMMtube	muscle
40	chr1:153755600-153756800	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:153755600-153756800	Active TSS	Fetal Stomach	stomach
42	chr1:153755800-153756200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:153755800-153756200	Active TSS	Primary B cells from peripheral blood	blood
44	chr1:153755800-153756200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:153755800-153756200	Active TSS	Placenta	Placenta
46	chr1:153755800-153756200	Active TSS	Gastric	stomach
47	chr1:153755800-153756200	Active TSS	Lung	lung
48	chr1:153755800-153756200	Active TSS	Small Intestine	intestine
49	chr1:153755800-153756400	Active TSS	H1 Cell Line	embryonic stem cell
50	chr1:153755800-153756400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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