Variant report

Variant	rs3130247
Chromosome Location	chr6:30515043-30515044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30514422..30516321-chr6:30710847..30712439,2	MCF-7	breast:
2	chr6:30447797..30449612-chr6:30512660..30515323,2	MCF-7	breast:
3	chr6:30515029..30517945-chr6:30687848..30689600,2	MCF-7	breast:
4	chr6:30481612..30484556-chr6:30512533..30515287,2	MCF-7	breast:
5	chr6:30456233..30458603-chr6:30513714..30516752,3	MCF-7	breast:
6	chr6:30511425..30515490-chr6:30579291..30582937,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137331	Chromatin interaction
ENSG00000235781	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000204592	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1059612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3094023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3094024	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094125	0.83[AMR][1000 genomes]
rs3094717	0.80[AMR][1000 genomes]
rs3095276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes]
rs3129972	0.90[AMR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes]
rs3130117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130658	0.83[AMR][1000 genomes]
rs3130660	0.83[AMR][1000 genomes]
rs3130668	0.91[AMR][1000 genomes]
rs3130670	0.83[AMR][1000 genomes]
rs3131112	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3132583	0.83[AMR][1000 genomes]
rs3132585	0.83[AMR][1000 genomes]
rs3132610	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132616	0.84[EUR][1000 genomes]
rs3132619	0.80[AMR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262143	0.86[EUR][1000 genomes]
rs9262146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3130247	HIST1H2BM	cis	cerebellum	SCAN
rs3130247	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3130247	HLA-A	cis	lymphoblastoid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30509800-30516200	Weak transcription	HMEC	breast
2	chr6:30509800-30519600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:30509800-30523000	Weak transcription	A549	lung
4	chr6:30510000-30521200	Weak transcription	Hela-S3	cervix
5	chr6:30510000-30522400	Weak transcription	Fetal Heart	heart
6	chr6:30510000-30523000	Weak transcription	Right Atrium	heart
7	chr6:30510200-30516200	Weak transcription	Colonic Mucosa	Colon
8	chr6:30510200-30519000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:30510400-30516200	Weak transcription	Fetal Kidney	kidney
10	chr6:30510800-30520000	Weak transcription	Fetal Brain Male	brain
11	chr6:30511600-30516000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:30511600-30522600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr6:30511800-30522600	Strong transcription	Placenta	Placenta
14	chr6:30512000-30515400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:30512400-30522000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:30512400-30522200	Strong transcription	Fetal Stomach	stomach
17	chr6:30512600-30515600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:30512600-30516200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:30512600-30517400	Weak transcription	NH-A	brain
20	chr6:30512600-30522400	Strong transcription	Fetal Thymus	thymus
21	chr6:30512800-30522000	Strong transcription	Fetal Intestine Small	intestine
22	chr6:30512800-30522000	Strong transcription	Lung	lung
23	chr6:30512800-30522000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr6:30512800-30522200	Strong transcription	HepG2	liver
25	chr6:30512800-30522400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:30512800-30522400	Strong transcription	Primary B cells from cord blood	blood
27	chr6:30512800-30522400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:30513000-30518800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:30513000-30520600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:30513000-30522000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:30513000-30522000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:30513000-30522200	Strong transcription	Fetal Intestine Large	intestine
33	chr6:30513200-30516000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:30513200-30516200	Strong transcription	Osteobl	bone
35	chr6:30513200-30517400	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr6:30513200-30522000	Strong transcription	Liver	Liver
37	chr6:30513200-30522000	Strong transcription	Brain Hippocampus Middle	brain
38	chr6:30513200-30522200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:30513200-30522200	Strong transcription	Brain Anterior Caudate	brain
40	chr6:30513200-30522200	Strong transcription	Fetal Muscle Leg	muscle
41	chr6:30513200-30522400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:30513200-30522400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:30513200-30522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:30513200-30522400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:30513200-30522400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:30513200-30522400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr6:30513200-30522600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr6:30513200-30522600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:30513200-30522600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr6:30513200-30522600	Strong transcription	Dnd41	blood

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