Variant report

Variant	rs11111765
Chromosome Location	chr12:104172519-104172520
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104166229..104169114-chr12:104169303..104172896,3	MCF-7	breast:
2	chr12:104171358..104174943-chr12:104233480..104236232,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10861094	0.85[AMR][1000 genomes]
rs10861095	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861096	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861097	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861104	0.92[ASN][1000 genomes]
rs11111750	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11111752	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11111754	0.85[AMR][1000 genomes]
rs11111755	0.85[AMR][1000 genomes]
rs11111757	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111758	0.91[AMR][1000 genomes]
rs11111759	0.90[AMR][1000 genomes]
rs11111762	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111763	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111767	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11111771	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11111778	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11111793	0.80[ASN][1000 genomes]
rs1565773	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs15918	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1866292	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1976256	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2292682	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3751204	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812805	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964298	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964823	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4964827	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4964830	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4981032	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4981036	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs751448	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs869993	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9132	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs954920	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899491	chr12:104151560-104175575	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11111765	RP11-341G23.4	cis	Adipose Subcutaneous	GTEx
rs11111765	RP11-341G23.4	cis	Artery Tibial	GTEx
rs11111765	RP11-341G23.4	cis	Artery Aorta	GTEx
rs11111765	RP11-341G23.4	cis	Thyroid	GTEx
rs11111765	RP11-341G23.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104155000-104178000	Weak transcription	Colonic Mucosa	Colon
4	chr12:104155200-104173400	Weak transcription	NHDF-Ad	bronchial
5	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
6	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:104163000-104178400	Strong transcription	NHEK	skin
8	chr12:104163200-104175200	Weak transcription	Psoas Muscle	Psoas
9	chr12:104163600-104174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:104163600-104185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:104165800-104173800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
14	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
15	chr12:104167000-104173400	Weak transcription	Right Ventricle	heart
16	chr12:104167000-104174400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:104167200-104173600	Weak transcription	Fetal Heart	heart
18	chr12:104167200-104176000	Weak transcription	Small Intestine	intestine
19	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:104167800-104173800	Strong transcription	A549	lung
21	chr12:104168000-104176800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:104168000-104178800	Weak transcription	Hela-S3	cervix
23	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
24	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:104168200-104173600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:104168400-104173600	Strong transcription	HMEC	breast
27	chr12:104168600-104180800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr12:104168800-104172600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:104168800-104172800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:104168800-104173200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:104168800-104174000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:104168800-104174000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr12:104168800-104174200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:104168800-104175400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:104169000-104174200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:104169000-104175000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:104169000-104176800	Strong transcription	Liver	Liver
38	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:104169200-104180200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:104169400-104174800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:104169600-104174200	Strong transcription	Colon Smooth Muscle	Colon
42	chr12:104169600-104184800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:104170000-104173600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:104170000-104173800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:104170200-104174400	Strong transcription	Fetal Stomach	stomach
46	chr12:104170400-104173200	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr12:104170400-104179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:104170400-104180400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr12:104170600-104173200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:104170600-104174000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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