Variant report

Variant	rs12134281
Chromosome Location	chr1:184528579-184528580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184515933..184517839-chr1:184525996..184528809,2	K562	blood:
2	chr1:184354217..184357197-chr1:184528030..184531247,3	MCF-7	breast:
3	chr1:184418404..184421283-chr1:184528359..184530284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116667	Chromatin interaction
ENSG00000271387	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10797979	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10911613	0.95[ASN][1000 genomes]
rs10911614	0.92[ASN][1000 genomes]
rs10911618	0.85[ASN][1000 genomes]
rs1339573	0.92[ASN][1000 genomes]
rs1416751	1.00[YRI][hapmap]
rs1569843	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1569844	0.96[ASN][1000 genomes]
rs1572767	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1856562	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1985703	0.96[ASN][1000 genomes]
rs1999996	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4651218	0.91[ASN][1000 genomes]
rs4651224	0.82[JPT][hapmap]
rs6424958	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6424959	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6424960	0.83[ASN][1000 genomes]
rs6667692	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6674023	0.92[ASN][1000 genomes]
rs6674115	0.92[ASN][1000 genomes]
rs6696816	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749214	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs946547	0.96[ASN][1000 genomes]

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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12134281	C1orf21	cis	Nerve Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184505800-184530800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:184505800-184531600	Weak transcription	Fetal Stomach	stomach
3	chr1:184511400-184530400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:184512200-184530200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:184512200-184543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:184512400-184530200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:184514400-184543800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:184515200-184531200	Weak transcription	NHLF	lung
9	chr1:184516400-184529000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:184520800-184542000	Weak transcription	Ovary	ovary
11	chr1:184521000-184530200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:184521000-184535800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:184521000-184547400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:184523000-184530200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:184524400-184529200	Enhancers	Psoas Muscle	Psoas
16	chr1:184524600-184531200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:184525000-184546000	Weak transcription	Brain Angular Gyrus	brain
18	chr1:184525200-184535200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:184525400-184535200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:184525600-184528600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:184525600-184536000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:184525600-184544000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:184525600-184545600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:184525800-184530200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:184525800-184530800	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:184525800-184531200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:184525800-184535200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:184526200-184531200	Weak transcription	Fetal Heart	heart
29	chr1:184526400-184531400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:184526400-184531600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:184526600-184529800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:184526600-184535600	Weak transcription	Left Ventricle	heart
33	chr1:184527000-184528600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:184527000-184528600	Enhancers	HMEC	breast
35	chr1:184527200-184530200	Weak transcription	Right Ventricle	heart
36	chr1:184527800-184528600	Enhancers	Right Atrium	heart
37	chr1:184527800-184530600	Weak transcription	Stomach Mucosa	stomach
38	chr1:184528000-184529200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:184528000-184530200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:184528200-184530200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:184528400-184530200	Weak transcription	Esophagus	oesophagus
42	chr1:184528400-184530200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:184528400-184530400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:184528400-184531400	Weak transcription	NHEK	skin

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