Variant report

Variant	rs12797540
Chromosome Location	chr11:63714835-63714836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63708705..63711538-chr11:63713648..63715559,2	K562	blood:
2	chr11:63705612..63708323-chr11:63713919..63715719,2	MCF-7	breast:
3	chr11:63679817..63682054-chr11:63713391..63715427,2	MCF-7	breast:
4	chr11:63713605..63716362-chr11:63716761..63720245,3	K562	blood:
5	chr11:63709555..63711338-chr11:63713486..63715543,2	MCF-7	breast:
6	chr11:63714375..63717341-chr11:63743522..63745649,2	K562	blood:
7	chr11:63712151..63714978-chr11:63752248..63754050,2	K562	blood:

Variant related genes	Relation type
ENSG00000167770	Chromatin interaction
ENSG00000167771	Chromatin interaction
ENSG00000110583	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10897459	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10897464	0.83[EUR][1000 genomes]
rs10897465	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897466	0.82[EUR][1000 genomes]
rs10897467	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10897469	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10897470	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231628	0.80[EUR][1000 genomes]
rs11231643	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11231646	0.90[EUR][1000 genomes]
rs11231653	0.84[EUR][1000 genomes]
rs11231655	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231662	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231663	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231664	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231670	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231671	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11600062	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11601228	0.81[EUR][1000 genomes]
rs11605797	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11607028	0.83[EUR][1000 genomes]
rs12417157	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12417507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12418000	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12421757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12786124	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12793201	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12794404	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12798491	0.84[EUR][1000 genomes]
rs12800703	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1386346	0.81[EUR][1000 genomes]
rs2129467	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224173	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2318110	0.87[EUR][1000 genomes]
rs3019785	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34134698	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34595065	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3740636	0.83[EUR][1000 genomes]
rs3740637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479975	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs492357	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4980499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4980500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4980501	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4980509	0.88[EUR][1000 genomes]
rs4980512	0.83[EUR][1000 genomes]
rs4980517	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4980530	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs501278	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs504060	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs509701	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs579669	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs581355	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67136175	0.85[EUR][1000 genomes]
rs7112348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728919	0.83[EUR][1000 genomes]
rs7926608	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7936614	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7950543	0.90[AFR][1000 genomes]
rs7951529	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv468590	chr11:63639881-63783352	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv555181	chr11:63639881-63783352	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv897629	chr11:63664882-63866959	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
7	nsv897639	chr11:63691049-63844683	Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 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	chr11:63707200-63724200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:63707400-63719600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:63707400-63721400	Weak transcription	Small Intestine	intestine
4	chr11:63707600-63719400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:63707600-63720200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:63707800-63719200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:63707800-63719600	Weak transcription	Lung	lung
8	chr11:63708000-63718200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:63708200-63723400	Weak transcription	NH-A	brain
10	chr11:63709000-63719200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:63709400-63718800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:63709600-63719600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr11:63709800-63718200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr11:63710600-63715400	Strong transcription	Primary T cells from cord blood	blood
15	chr11:63712000-63716800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:63712400-63717600	Strong transcription	Dnd41	blood
17	chr11:63712600-63716400	Strong transcription	Thymus	Thymus
18	chr11:63712600-63717000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr11:63713000-63717200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:63713200-63716800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:63713200-63718400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:63713200-63719800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:63713200-63719800	Weak transcription	Aorta	Aorta
24	chr11:63713200-63725400	Weak transcription	Psoas Muscle	Psoas
25	chr11:63713200-63725800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:63713400-63715800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:63713400-63715800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr11:63713400-63716800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:63713400-63717000	Strong transcription	Fetal Brain Female	brain
30	chr11:63713400-63717200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:63713400-63718400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:63713400-63718400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:63713400-63719400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:63713400-63719600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:63713400-63719600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:63713400-63719800	Weak transcription	Brain Substantia Nigra	brain
37	chr11:63713400-63721200	Weak transcription	Stomach Mucosa	stomach
38	chr11:63713400-63721600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:63713400-63721600	Weak transcription	Ovary	ovary
40	chr11:63713400-63724200	Strong transcription	K562	blood
41	chr11:63713400-63725200	Strong transcription	Fetal Intestine Small	intestine
42	chr11:63713400-63725400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:63713400-63725800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:63713400-63726200	Strong transcription	Fetal Stomach	stomach
45	chr11:63713400-63726800	Weak transcription	Fetal Brain Male	brain
46	chr11:63713400-63733800	Weak transcription	Right Atrium	heart
47	chr11:63713600-63715000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:63713600-63715200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:63713600-63715800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:63713600-63716600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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