Variant report

Variant	rs10778286
Chromosome Location	chr12:104178731-104178732
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104178636..104180567-chr12:104180995..104183516,2	K562	blood:
2	chr12:104178670..104180428-chr12:104186156..104188204,2	K562	blood:
3	chr12:104177175..104180567-chr12:104180842..104183516,3	K562	blood:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10735389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778290	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10861106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10861107	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs10861112	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11111774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111801	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12307138	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs12425205	0.85[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1973658	0.98[ASN][1000 genomes]
rs3812804	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4248827	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300459	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964629	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4964818	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4981034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135173	0.84[ASN][1000 genomes]
rs7970553	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9739384	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[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	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
10	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10778286	RP11-341G23.4	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 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	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
4	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:104163600-104185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
8	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
9	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:104168000-104178800	Weak transcription	Hela-S3	cervix
11	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
12	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:104168600-104180800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:104169200-104180200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:104169600-104184800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:104170400-104179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:104170400-104180400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:104170600-104179400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:104171400-104188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:104171600-104187400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
24	chr12:104171800-104187600	Weak transcription	Fetal Brain Female	brain
25	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:104172400-104186400	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:104173000-104179400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:104173400-104179000	Strong transcription	Ovary	ovary
30	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:104174000-104180400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:104174000-104180400	Strong transcription	HMEC	breast
33	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:104174200-104179200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:104174200-104179200	Weak transcription	NHDF-Ad	bronchial
36	chr12:104174200-104185200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:104174200-104186200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:104174400-104179800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr12:104174800-104180400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:104175000-104179800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr12:104175000-104180600	Strong transcription	HSMM	muscle
42	chr12:104175000-104187000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:104175200-104179200	Strong transcription	A549	lung
44	chr12:104175200-104190000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:104175400-104179600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:104175600-104179200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:104175800-104179200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:104175800-104180400	Strong transcription	Colon Smooth Muscle	Colon
49	chr12:104175800-104180600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:104176200-104179000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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