Variant report

Variant	rs12127954
Chromosome Location	chr1:212408974-212408975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212408314..212411280-chr1:212781747..212784026,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1011232	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10735509	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10779577	0.88[ASN][1000 genomes]
rs10863955	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs10863956	0.90[ASN][1000 genomes]
rs10863957	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10863958	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11119873	0.85[EUR][1000 genomes]
rs11119886	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11119888	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11119890	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11119891	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11119893	0.84[ASN][1000 genomes]
rs11119918	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[AFR][1000 genomes]
rs11119921	1.00[AFR][1000 genomes]
rs11119928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12116770	1.00[AFR][1000 genomes]
rs12119183	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12124065	1.00[EUR][1000 genomes]
rs12132912	0.85[EUR][1000 genomes]
rs12133134	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12133636	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12134276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12134599	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12145377	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12145451	0.88[ASN][1000 genomes]
rs12146141	0.86[ASN][1000 genomes]
rs17018777	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs17018847	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17018853	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2236598	0.84[EUR][1000 genomes]
rs3754142	1.00[CEU][hapmap]
rs399429	0.81[ASN][1000 genomes]
rs4951580	0.85[ASN][1000 genomes]
rs61260530	0.86[ASN][1000 genomes]
rs884923	0.88[ASN][1000 genomes]
rs903119	0.95[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212401800-212409000	Weak transcription	Gastric	stomach
2	chr1:212403400-212409000	Weak transcription	Fetal Intestine Large	intestine
3	chr1:212403600-212409600	Weak transcription	Liver	Liver
4	chr1:212404800-212410800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr1:212405200-212410600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:212405600-212409000	Weak transcription	Esophagus	oesophagus
7	chr1:212405600-212414800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:212405600-212416400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:212406400-212411000	Enhancers	HSMMtube	muscle
10	chr1:212406600-212409200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:212406600-212410800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:212406800-212409800	Enhancers	Fetal Muscle Leg	muscle
13	chr1:212406800-212410400	Enhancers	HSMM	muscle
14	chr1:212406800-212410600	Enhancers	Stomach Mucosa	stomach
15	chr1:212407000-212409200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:212407200-212410400	Enhancers	Left Ventricle	heart
17	chr1:212407600-212409200	Enhancers	NHLF	lung
18	chr1:212407600-212410000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:212407600-212412400	Enhancers	Duodenum Mucosa	Duodenum
20	chr1:212407800-212409600	Enhancers	Right Atrium	heart
21	chr1:212407800-212409800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:212407800-212410400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:212407800-212412800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:212408000-212409000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:212408000-212409200	Weak transcription	Right Ventricle	heart
26	chr1:212408000-212410600	Enhancers	Fetal Heart	heart
27	chr1:212408000-212411600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:212408000-212411800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:212408000-212413000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:212408200-212409600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr1:212408200-212409800	Enhancers	Small Intestine	intestine
32	chr1:212408200-212415400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:212408400-212409800	Enhancers	Lung	lung
34	chr1:212408400-212410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:212408400-212411600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:212408400-212415600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:212408600-212409000	Enhancers	Pancreas	Pancrea
38	chr1:212408600-212409000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr1:212408600-212409200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:212408600-212409200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:212408600-212409400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:212408600-212409400	Weak transcription	Psoas Muscle	Psoas
43	chr1:212408600-212409600	Weak transcription	Colonic Mucosa	Colon
44	chr1:212408600-212410200	Weak transcription	HepG2	liver
45	chr1:212408600-212410400	Weak transcription	HMEC	breast
46	chr1:212408600-212410800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:212408600-212410800	Weak transcription	GM12878-XiMat	blood
48	chr1:212408600-212411000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:212408600-212411000	Weak transcription	NHDF-Ad	bronchial
50	chr1:212408600-212411200	Weak transcription	A549	lung

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