Variant report

Variant	rs12061642
Chromosome Location	chr1:228586236-228586237
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228578293-228588731	K562	blood:	n/a	n/a
2	POLR2A	chr1:228585634-228586547	K562	blood:	n/a	n/a
3	POLR2A	chr1:228585671-228586612	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228582272..228585110-chr1:228585474..228588026,2	MCF-7	breast:
2	chr1:228585905..228588750-chr1:228676571..228678465,2	MCF-7	breast:
3	chr1:228540204..228544343-chr1:228583648..228586877,3	K562	blood:
4	chr1:228585219..228604537-chr1:228641966..228650471,45	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM11	TF binding region
ENSG00000196890	Chromatin interaction
ENSG00000168159	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000266174	Chromatin interaction
ENSG00000154358	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10157289	0.91[EUR][1000 genomes]
rs10158088	0.81[EUR][1000 genomes]
rs10158354	0.91[EUR][1000 genomes]
rs10158680	0.91[EUR][1000 genomes]
rs10916313	0.86[ASN][1000 genomes]
rs1150917	0.92[ASN][1000 genomes]
rs1150918	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11555960	0.89[EUR][1000 genomes]
rs11581974	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11587839	0.86[ASN][1000 genomes]
rs1188473	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1188474	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1188475	0.89[AMR][1000 genomes]
rs1188482	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1188483	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1188485	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1188487	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1188488	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1188489	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12027720	0.88[EUR][1000 genomes]
rs12031395	0.91[EUR][1000 genomes]
rs12061490	0.91[EUR][1000 genomes]
rs12061733	0.83[EUR][1000 genomes]
rs12065660	0.91[EUR][1000 genomes]
rs12065815	0.91[EUR][1000 genomes]
rs12082349	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12085738	0.94[EUR][1000 genomes]
rs12089997	0.91[EUR][1000 genomes]
rs12093491	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12094956	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12096217	0.84[EUR][1000 genomes]
rs12691493	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12725863	0.86[ASN][1000 genomes]
rs12735877	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12751024	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12760907	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13373984	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2230656	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34090141	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34673199	0.91[EUR][1000 genomes]
rs35155240	0.91[EUR][1000 genomes]
rs35670307	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35711644	0.93[EUR][1000 genomes]
rs3738687	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795810	0.87[EUR][1000 genomes]
rs3795814	0.91[EUR][1000 genomes]
rs4065231	0.90[EUR][1000 genomes]
rs4581279	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653551	0.86[ASN][1000 genomes]
rs4653552	0.86[ASN][1000 genomes]
rs4653960	0.83[ASN][1000 genomes]
rs474600	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491670	0.86[EUR][1000 genomes]
rs493950	0.88[EUR][1000 genomes]
rs493954	0.89[EUR][1000 genomes]
rs494154	0.89[EUR][1000 genomes]
rs503203	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs503391	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs505129	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513467	0.89[EUR][1000 genomes]
rs532465	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs538604	0.88[EUR][1000 genomes]
rs538851	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs541959	0.91[EUR][1000 genomes]
rs56174824	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs564309	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs572442	0.93[EUR][1000 genomes]
rs573128	0.93[EUR][1000 genomes]
rs58462432	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61825312	0.91[EUR][1000 genomes]
rs61825336	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61825338	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827276	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6426501	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6659690	0.86[ASN][1000 genomes]
rs6666241	0.86[ASN][1000 genomes]
rs7513530	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7524236	0.86[ASN][1000 genomes]
rs7555386	0.86[ASN][1000 genomes]
rs9787095	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv468271	chr1:228464248-228601638	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv468283	chr1:228464248-228601638	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv468294	chr1:228464248-228601638	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv549295	chr1:228464248-228601638	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
14	nsv470780	chr1:228464248-228606965	Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
16	nsv873280	chr1:228500627-228603029	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
18	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
19	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
20	nsv508697	chr1:228540037-228622614	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
21	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 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	chr1:228567000-228592800	Weak transcription	Fetal Kidney	kidney
2	chr1:228571000-228591600	Weak transcription	Fetal Brain Male	brain
3	chr1:228577000-228592600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:228577400-228590800	Weak transcription	Right Atrium	heart
5	chr1:228579000-228590600	Strong transcription	Gastric	stomach
6	chr1:228579000-228591200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:228579000-228592000	Strong transcription	Fetal Stomach	stomach
8	chr1:228579200-228588400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:228579400-228590600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:228579400-228590800	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:228579400-228591800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:228579400-228592000	Strong transcription	Fetal Intestine Small	intestine
13	chr1:228579600-228591000	Strong transcription	Liver	Liver
14	chr1:228579600-228591600	Strong transcription	Fetal Brain Female	brain
15	chr1:228579600-228591600	Strong transcription	Thymus	Thymus
16	chr1:228579600-228592000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:228579800-228588600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:228579800-228590800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:228579800-228591800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:228579800-228591800	Strong transcription	Brain Germinal Matrix	brain
21	chr1:228579800-228591800	Strong transcription	Fetal Thymus	thymus
22	chr1:228579800-228592600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:228580000-228591200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:228580000-228591800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:228580000-228592000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:228580200-228591800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:228580800-228590600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:228581000-228592400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:228581200-228592800	Weak transcription	Psoas Muscle	Psoas
30	chr1:228581400-228589400	Strong transcription	Dnd41	blood
31	chr1:228581600-228586400	Strong transcription	Primary B cells from cord blood	blood
32	chr1:228581600-228591200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:228581600-228591200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:228581600-228592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:228581600-228592000	Strong transcription	A549	lung
36	chr1:228581800-228586400	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr1:228581800-228587200	Strong transcription	Brain Cingulate Gyrus	brain
38	chr1:228581800-228590000	Strong transcription	Esophagus	oesophagus
39	chr1:228581800-228590000	Strong transcription	NHEK	skin
40	chr1:228581800-228591200	Strong transcription	Fetal Intestine Large	intestine
41	chr1:228582000-228587000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:228582000-228589200	Strong transcription	Pancreas	Pancrea
43	chr1:228582000-228590200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:228582000-228590400	Strong transcription	Right Ventricle	heart
45	chr1:228582000-228590800	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:228582000-228591000	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:228582000-228591200	Strong transcription	Ovary	ovary
48	chr1:228582000-228591200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:228582000-228591800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:228582000-228592200	Weak transcription	Fetal Heart	heart

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