Variant report

Variant	rs11111786
Chromosome Location	chr12:104189057-104189058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr12:104188933-104189176	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr12:104188892-104189208	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104186877..104189949-chr12:104233437..104236104,3	MCF-7	breast:
2	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:

Variant related genes	Relation type
NT5DC3	TF binding region
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10861102	0.96[AFR][1000 genomes]
rs10861103	0.96[AFR][1000 genomes]
rs10861104	0.95[EUR][1000 genomes]
rs10861105	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861109	0.82[EUR][1000 genomes]
rs11111772	0.94[AFR][1000 genomes]
rs11111773	0.96[AFR][1000 genomes]
rs11111775	0.96[AFR][1000 genomes]
rs11111776	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11111779	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111781	0.96[AFR][1000 genomes]
rs11111782	0.96[AFR][1000 genomes]
rs11111783	0.96[AFR][1000 genomes]
rs11111787	0.94[AFR][1000 genomes]
rs11111788	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111789	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111791	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111792	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111793	0.87[EUR][1000 genomes]
rs11111795	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11111796	0.84[EUR][1000 genomes]
rs12228207	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12229276	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12424737	0.88[AFR][1000 genomes]
rs12830701	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1370777	0.88[AFR][1000 genomes]
rs1370778	0.96[AFR][1000 genomes]
rs1370779	0.96[AFR][1000 genomes]
rs1866293	0.96[AFR][1000 genomes]
rs1866294	0.96[AFR][1000 genomes]
rs1866295	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1866296	0.96[AFR][1000 genomes]
rs1968513	0.96[AFR][1000 genomes]
rs2888792	0.96[AFR][1000 genomes]
rs34307072	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35371470	0.84[EUR][1000 genomes]
rs35945096	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36034617	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3812803	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3935416	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4964289	0.84[EUR][1000 genomes]
rs4964623	0.81[EUR][1000 genomes]
rs4964780	0.84[EUR][1000 genomes]
rs4964794	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964805	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4964806	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4964812	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964813	0.96[AFR][1000 genomes]
rs4964814	0.96[AFR][1000 genomes]
rs4964819	0.96[AFR][1000 genomes]
rs4964820	0.96[AFR][1000 genomes]
rs5001722	0.93[AFR][1000 genomes]
rs58421738	0.96[AFR][1000 genomes]
rs67825151	0.84[EUR][1000 genomes]
rs7134701	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7312606	0.96[AFR][1000 genomes]
rs7312825	0.96[AFR][1000 genomes]
rs73192049	0.90[AFR][1000 genomes]
rs73192053	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs934843	0.96[AFR][1000 genomes]
rs934845	0.96[AFR][1000 genomes]
rs934846	0.96[AFR][1000 genomes]
rs934847	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9706225	0.96[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11111786	RP11-341G23.4	cis	Artery Tibial	GTEx
rs11111786	RP11-341G23.4	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
2	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
4	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
9	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:104175200-104190000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:104178600-104193400	Weak transcription	Left Ventricle	heart
16	chr12:104178800-104194000	Weak transcription	Brain Angular Gyrus	brain
17	chr12:104178800-104194200	Weak transcription	Esophagus	oesophagus
18	chr12:104179000-104190600	Weak transcription	Gastric	stomach
19	chr12:104179000-104193200	Weak transcription	Spleen	Spleen
20	chr12:104179000-104193600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:104179400-104191400	Weak transcription	Hela-S3	cervix
22	chr12:104179400-104193800	Weak transcription	Fetal Kidney	kidney
23	chr12:104179800-104192800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:104179800-104193800	Weak transcription	NHDF-Ad	bronchial
25	chr12:104183600-104192800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:104183800-104193600	Weak transcription	Stomach Mucosa	stomach
27	chr12:104184800-104190400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:104184800-104192600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:104184800-104193400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:104185000-104189200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:104185000-104190800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr12:104185000-104190800	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:104185000-104191200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr12:104185000-104191200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:104185000-104191200	Strong transcription	Aorta	Aorta
36	chr12:104185200-104189200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:104185200-104189200	Strong transcription	NHEK	skin
38	chr12:104185200-104189400	Strong transcription	Liver	Liver
39	chr12:104185200-104190800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:104185200-104191000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr12:104185200-104191200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:104185200-104192000	Strong transcription	A549	lung
43	chr12:104185200-104192400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:104185200-104192600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:104185400-104189200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:104185400-104189400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr12:104185400-104190200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:104185400-104190800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:104185400-104190800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:104185400-104191000	Strong transcription	NHLF	lung

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