Variant report

Variant	rs12060029
Chromosome Location	chr1:212571575-212571576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212570221..212572169-chr1:212580241..212582437,2	K562	blood:
2	chr1:212569599..212572522-chr1:212576653..212579387,2	K562	blood:
3	chr1:212569162..212572404-chr1:212781980..212783777,4	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10863961	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs10863963	1.00[CHB][hapmap]
rs11119919	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11119920	0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11119924	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11119929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576437	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11576769	0.84[ASN][1000 genomes]
rs11580285	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11584189	0.82[ASN][1000 genomes]
rs11587555	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11588867	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11589817	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11590242	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11590672	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12062818	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090970	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12095810	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12096035	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12411213	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12726409	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12727947	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12728266	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12734895	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12736502	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12743785	0.86[CHB][hapmap]
rs12745269	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12756678	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1470390	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1493600	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17721302	1.00[CHB][hapmap]
rs2120770	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2297306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358454	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs2884465	0.92[ASN][1000 genomes]
rs2884466	0.92[ASN][1000 genomes]
rs34080686	0.84[ASN][1000 genomes]
rs4951595	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661987	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6667199	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72754339	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518399	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7531219	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]

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	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
2	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
2	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
3	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
4	chr1:212553200-212578400	Weak transcription	K562	blood
5	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
6	chr1:212558600-212578800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:212558600-212580000	Weak transcription	Left Ventricle	heart
8	chr1:212560200-212578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:212560400-212580200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:212560600-212578200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:212560600-212578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:212560600-212580200	Weak transcription	HSMMtube	muscle
13	chr1:212560600-212582000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:212560600-212582000	Weak transcription	Gastric	stomach
15	chr1:212561000-212575400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:212561000-212578000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:212561000-212579800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:212561000-212579800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:212561000-212580000	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:212561000-212582400	Weak transcription	Aorta	Aorta
21	chr1:212561200-212572000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:212562000-212578400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:212564200-212578800	Weak transcription	Esophagus	oesophagus
24	chr1:212564400-212575400	Weak transcription	Thymus	Thymus
25	chr1:212564600-212576200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:212564600-212577800	Weak transcription	Spleen	Spleen
27	chr1:212564600-212578600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:212564600-212579800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:212569000-212572200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr1:212569400-212572000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr1:212569400-212572400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr1:212569400-212572800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:212569600-212582600	Weak transcription	Ovary	ovary
34	chr1:212569800-212571600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
35	chr1:212569800-212571800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:212569800-212572000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
37	chr1:212570000-212571600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr1:212570000-212571600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:212570000-212572600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:212570000-212572600	ZNF genes & repeats	Dnd41	blood
41	chr1:212570000-212572600	ZNF genes & repeats	GM12878-XiMat	blood
42	chr1:212570200-212572000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:212570200-212572000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:212570400-212572400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr1:212570400-212572600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:212570400-212573000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
47	chr1:212570400-212578800	Weak transcription	Fetal Stomach	stomach
48	chr1:212570600-212571600	ZNF genes & repeats	Primary T cells from cord blood	blood
49	chr1:212570600-212572200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:212570600-212574400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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