Variant report

Variant	rs3131062
Chromosome Location	chr6:30763714-30763715
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30707638..30712527-chr6:30761800..30767458,10	K562	blood:
2	chr6:30758839..30761709-chr6:30762940..30765835,2	MCF-7	breast:
3	chr6:30747273..30752496-chr6:30759061..30765017,9	K562	blood:
4	chr6:30705811..30713504-chr6:30753060..30768565,33	MCF-7	breast:
5	chr6:30757280..30759870-chr6:30760366..30765437,6	K562	blood:
6	chr6:30762133..30768787-chr6:30785989..30790050,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228022	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11757629	0.94[ASN][1000 genomes]
rs12111310	0.82[ASN][1000 genomes]
rs1264352	0.97[ASN][1000 genomes]
rs17189329	0.81[ASN][1000 genomes]
rs2894045	0.94[ASN][1000 genomes]
rs3095337	0.81[ASN][1000 genomes]
rs3129986	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131064	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926530	0.94[ASN][1000 genomes]
rs9262207	0.90[ASN][1000 genomes]
rs9262211	0.90[ASN][1000 genomes]
rs9262215	0.90[ASN][1000 genomes]
rs9262216	0.90[ASN][1000 genomes]
rs9262217	0.90[ASN][1000 genomes]
rs9262218	0.90[ASN][1000 genomes]
rs9262219	0.88[ASN][1000 genomes]
rs9468824	0.88[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	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	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv1023695	chr6:30754540-30773349	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3131062	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30751000-30769800	Weak transcription	Right Ventricle	heart
2	chr6:30757600-30768400	Weak transcription	Hela-S3	cervix
3	chr6:30758000-30765600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:30758400-30764200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr6:30759200-30768800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:30760600-30764400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:30761600-30764200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:30761600-30781000	Weak transcription	Small Intestine	intestine
9	chr6:30761800-30763800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr6:30761800-30764200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:30761800-30772000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr6:30762000-30764000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:30762000-30764200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:30762000-30764200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr6:30762000-30764400	Enhancers	K562	blood
16	chr6:30762000-30766200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:30762000-30766800	Weak transcription	HUVEC	blood vessel
18	chr6:30762000-30768600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:30762400-30766200	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:30762400-30766800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:30762600-30766200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:30762600-30766200	Weak transcription	Fetal Lung	lung
23	chr6:30762600-30766200	Weak transcription	NHLF	lung
24	chr6:30762600-30767000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:30762600-30768800	Weak transcription	Fetal Stomach	stomach
26	chr6:30762800-30763800	Weak transcription	Primary B cells from cord blood	blood
27	chr6:30763000-30764000	Weak transcription	Primary T cells from cord blood	blood
28	chr6:30763000-30765800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:30763000-30766800	Weak transcription	Placenta	Placenta
30	chr6:30763200-30768600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:30763400-30764000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:30763400-30764400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:30763400-30764400	Enhancers	HMEC	breast
34	chr6:30763400-30764400	Enhancers	NHEK	skin
35	chr6:30763600-30763800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:30763600-30763800	Enhancers	GM12878-XiMat	blood
37	chr6:30763600-30764200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr6:30763600-30764200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:30763600-30764400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:30763600-30771000	Enhancers	HepG2	liver
41	chr6:30763600-30772000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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