Variant report

Variant	rs11111788
Chromosome Location	chr12:104190153-104190154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104183709..104186598-chr12:104189875..104192288,3	K562	blood:
2	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10861094	0.83[ASN][1000 genomes]
rs10861102	0.98[AFR][1000 genomes]
rs10861103	0.98[AFR][1000 genomes]
rs10861104	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861109	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11111754	0.83[ASN][1000 genomes]
rs11111755	0.83[ASN][1000 genomes]
rs11111758	0.81[ASN][1000 genomes]
rs11111772	0.96[AFR][1000 genomes]
rs11111773	0.98[AFR][1000 genomes]
rs11111775	0.98[AFR][1000 genomes]
rs11111776	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11111779	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11111781	0.98[AFR][1000 genomes]
rs11111782	0.98[AFR][1000 genomes]
rs11111783	0.98[AFR][1000 genomes]
rs11111786	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111787	0.96[AFR][1000 genomes]
rs11111789	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111791	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111792	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111793	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11111795	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11111796	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12228207	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12229276	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12424737	0.91[AFR][1000 genomes]
rs12830701	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1370777	0.90[AFR][1000 genomes]
rs1370778	0.98[AFR][1000 genomes]
rs1370779	0.98[AFR][1000 genomes]
rs1866293	0.98[AFR][1000 genomes]
rs1866294	0.98[AFR][1000 genomes]
rs1866295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1866296	0.98[AFR][1000 genomes]
rs1968513	0.98[AFR][1000 genomes]
rs2888792	0.98[AFR][1000 genomes]
rs34307072	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35371470	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35746861	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35945096	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36034617	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812803	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3935416	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4964289	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4964623	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4964780	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4964786	0.81[ASN][1000 genomes]
rs4964794	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964805	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964806	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964813	0.98[AFR][1000 genomes]
rs4964814	0.98[AFR][1000 genomes]
rs4964819	0.98[AFR][1000 genomes]
rs4964820	0.98[AFR][1000 genomes]
rs5001722	0.95[AFR][1000 genomes]
rs58421738	0.98[AFR][1000 genomes]
rs67825151	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7134701	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7312606	0.98[AFR][1000 genomes]
rs7312825	0.98[AFR][1000 genomes]
rs73192049	0.93[AFR][1000 genomes]
rs73192053	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs934843	0.98[AFR][1000 genomes]
rs934845	0.98[AFR][1000 genomes]
rs934846	0.98[AFR][1000 genomes]
rs934847	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9706225	0.98[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
rs11111788	RP11-341G23.4	cis	Artery Tibial	GTEx
rs11111788	RP11-341G23.4	cis	Thyroid	GTEx

Chromatin state (count:119 , 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	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:104178600-104193400	Weak transcription	Left Ventricle	heart
15	chr12:104178800-104194000	Weak transcription	Brain Angular Gyrus	brain
16	chr12:104178800-104194200	Weak transcription	Esophagus	oesophagus
17	chr12:104179000-104190600	Weak transcription	Gastric	stomach
18	chr12:104179000-104193200	Weak transcription	Spleen	Spleen
19	chr12:104179000-104193600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:104179400-104191400	Weak transcription	Hela-S3	cervix
21	chr12:104179400-104193800	Weak transcription	Fetal Kidney	kidney
22	chr12:104179800-104192800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:104179800-104193800	Weak transcription	NHDF-Ad	bronchial
24	chr12:104183600-104192800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:104183800-104193600	Weak transcription	Stomach Mucosa	stomach
26	chr12:104184800-104190400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:104184800-104192600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:104184800-104193400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:104185000-104190800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:104185000-104190800	Strong transcription	Fetal Muscle Leg	muscle
31	chr12:104185000-104191200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr12:104185000-104191200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:104185000-104191200	Strong transcription	Aorta	Aorta
34	chr12:104185200-104190800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr12:104185200-104191000	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr12:104185200-104191200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:104185200-104192000	Strong transcription	A549	lung
38	chr12:104185200-104192400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:104185200-104192600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:104185400-104190200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:104185400-104190800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:104185400-104190800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:104185400-104191000	Strong transcription	NHLF	lung
44	chr12:104185400-104192800	Strong transcription	HSMM	muscle
45	chr12:104185400-104193600	Strong transcription	Primary T cells from cord blood	blood
46	chr12:104185400-104193800	Strong transcription	K562	blood
47	chr12:104185600-104190800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:104185600-104190800	Strong transcription	Fetal Intestine Large	intestine
49	chr12:104185600-104190800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr12:104185600-104191200	Strong transcription	Osteobl	bone

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