Variant report

Variant	rs3094222
Chromosome Location	chr6:31081434-31081435
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	RCOR1	chr6:31081316-31083395	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31080693..31083957-chr6:31087484..31089976,3	K562	blood:
2	chr6:30850897..30852602-chr6:31080609..31083224,2	MCF-7	breast:
3	chr6:31079457..31085209-chr6:31085850..31092700,13	MCF-7	breast:
4	chr6:31050562..31052756-chr6:31081245..31083912,2	MCF-7	breast:

Variant related genes	Relation type
C6orf15	TF binding region
PSORS1C1	TF binding region
ENSG00000204539	Chromatin interaction
ENSG00000222895	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2233980	0.95[EUR][1000 genomes]
rs28754323	0.81[AFR][1000 genomes]
rs3094669	0.88[EUR][1000 genomes]
rs3094671	0.90[EUR][1000 genomes]
rs3095311	0.90[EUR][1000 genomes]
rs3130544	0.86[EUR][1000 genomes]
rs3130557	1.00[EUR][1000 genomes]
rs3130562	1.00[EUR][1000 genomes]
rs3130566	0.88[EUR][1000 genomes]
rs3130985	1.00[EUR][1000 genomes]
rs3131010	0.88[EUR][1000 genomes]
rs3132541	1.00[EUR][1000 genomes]
rs3132566	0.88[EUR][1000 genomes]
rs7750641	0.90[EUR][1000 genomes]
rs9295952	0.83[AFR][1000 genomes]
rs9501051	0.81[AFR][1000 genomes]
rs9501052	0.85[AFR][1000 genomes]
rs9501054	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv462746	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv601489	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv601490	chr6:31079264-31084435	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3094222	C4A	cis	Esophagus Mucosa	GTEx
rs3094222	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3094222	LINC00243	cis	Whole Blood	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31076800-31082200	Weak transcription	Spleen	Spleen
2	chr6:31077600-31082600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:31078200-31082200	Weak transcription	Gastric	stomach
4	chr6:31078800-31082200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:31078800-31082200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:31079000-31081600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:31079000-31081600	Weak transcription	A549	lung
8	chr6:31079200-31081800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:31079600-31082800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr6:31079800-31081800	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr6:31080000-31082200	Enhancers	HSMMtube	muscle
12	chr6:31080200-31082400	Enhancers	HMEC	breast
13	chr6:31080400-31081600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:31080400-31081600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:31080400-31082000	Enhancers	HSMM	muscle
16	chr6:31080400-31082200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:31080600-31081600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:31080600-31081600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:31080600-31082000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:31080600-31083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:31080800-31082200	Enhancers	NHDF-Ad	bronchial
22	chr6:31081000-31083200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr6:31081200-31081800	Enhancers	Hela-S3	cervix
24	chr6:31081200-31082000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:31081200-31082200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:31081200-31082200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:31081200-31082200	Enhancers	NH-A	brain
28	chr6:31081200-31082200	Enhancers	NHEK	skin
29	chr6:31081200-31082200	Enhancers	NHLF	lung
30	chr6:31081200-31082400	Enhancers	Right Atrium	heart
31	chr6:31081200-31082600	Enhancers	Adipose Nuclei	Adipose
32	chr6:31081200-31082600	Enhancers	Stomach Mucosa	stomach
33	chr6:31081200-31082800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:31081200-31082800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr6:31081200-31083200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr6:31081200-31083400	Enhancers	Brain Hippocampus Middle	brain
37	chr6:31081200-31083400	Enhancers	Brain Substantia Nigra	brain
38	chr6:31081200-31085400	Enhancers	Right Ventricle	heart
39	chr6:31081400-31081800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:31081400-31082200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:31081400-31082200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:31081400-31082200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:31081400-31082200	Enhancers	Colon Smooth Muscle	Colon
44	chr6:31081400-31082400	Enhancers	Colonic Mucosa	Colon
45	chr6:31081400-31082600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:31081400-31082600	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr6:31081400-31083800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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