Variant report

Variant	rs3130658
Chromosome Location	chr6:30701092-30701093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30700251..30701939-chr6:30758549..30760829,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1059612	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1264351	0.83[AMR][1000 genomes]
rs1264373	0.83[AMR][1000 genomes]
rs3094023	0.83[AMR][1000 genomes]
rs3094118	0.85[EUR][1000 genomes]
rs3094125	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095276	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3095326	0.87[EUR][1000 genomes]
rs3095327	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3095328	0.89[EUR][1000 genomes]
rs3095332	0.89[EUR][1000 genomes]
rs3095334	0.83[EUR][1000 genomes]
rs3129972	0.90[EUR][1000 genomes]
rs3129973	0.87[EUR][1000 genomes]
rs3129974	0.89[EUR][1000 genomes]
rs3129977	0.82[EUR][1000 genomes]
rs3129978	0.83[EUR][1000 genomes]
rs3129984	0.81[EUR][1000 genomes]
rs3130117	0.83[AMR][1000 genomes]
rs3130247	0.83[AMR][1000 genomes]
rs3130660	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130665	0.85[EUR][1000 genomes]
rs3130668	0.81[EUR][1000 genomes]
rs3130673	0.83[EUR][1000 genomes]
rs3132582	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132583	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132585	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132599	0.83[EUR][1000 genomes]
rs3132600	0.87[EUR][1000 genomes]
rs3132603	0.83[EUR][1000 genomes]
rs3132605	0.83[EUR][1000 genomes]
rs9262126	0.95[EUR][1000 genomes]
rs9262130	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9262132	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9262135	0.95[EUR][1000 genomes]
rs9262141	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262142	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262143	0.92[EUR][1000 genomes]
rs9262146	0.83[AMR][1000 genomes];0.92[EUR][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	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv970736	chr6:30692055-30710740	Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
10	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130658	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30690000-30709600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30690400-30709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:30690600-30701200	Strong transcription	Brain Angular Gyrus	brain
4	chr6:30690600-30703800	Strong transcription	Lung	lung
5	chr6:30691000-30703800	Strong transcription	Brain Cingulate Gyrus	brain
6	chr6:30692600-30708200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:30693200-30708800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:30693400-30709000	Strong transcription	Fetal Stomach	stomach
9	chr6:30693800-30704200	Strong transcription	Fetal Lung	lung
10	chr6:30693800-30709000	Strong transcription	Fetal Brain Female	brain
11	chr6:30694000-30708800	Weak transcription	Fetal Brain Male	brain
12	chr6:30694200-30705600	Weak transcription	Small Intestine	intestine
13	chr6:30694400-30707800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:30694600-30704800	Weak transcription	Right Atrium	heart
15	chr6:30695400-30708200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:30695400-30709000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:30695400-30709200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:30695600-30707800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:30696200-30707400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:30696400-30709000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:30696600-30706800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:30696800-30705600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:30696800-30707400	Strong transcription	NHLF	lung
24	chr6:30697000-30707600	Strong transcription	Osteobl	bone
25	chr6:30697000-30707800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:30697000-30708600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:30697000-30709200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:30697800-30705800	Weak transcription	NH-A	brain
29	chr6:30698200-30705200	Weak transcription	Fetal Kidney	kidney
30	chr6:30698400-30701200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:30698400-30703000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:30698400-30703800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:30698600-30702600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:30698600-30704800	Weak transcription	Fetal Heart	heart
35	chr6:30698600-30705600	Weak transcription	Psoas Muscle	Psoas
36	chr6:30698800-30702400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:30698800-30702400	Weak transcription	Primary T cells from cord blood	blood
38	chr6:30698800-30702400	Weak transcription	K562	blood
39	chr6:30698800-30703200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:30698800-30704200	Strong transcription	Thymus	Thymus
41	chr6:30698800-30704800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:30698800-30705000	Weak transcription	HMEC	breast
43	chr6:30698800-30706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:30698800-30707400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:30698800-30707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:30698800-30708200	Strong transcription	Liver	Liver
47	chr6:30698800-30708200	Strong transcription	Brain Hippocampus Middle	brain
48	chr6:30698800-30708200	Strong transcription	Fetal Intestine Small	intestine
49	chr6:30698800-30708600	Strong transcription	Brain Anterior Caudate	brain
50	chr6:30698800-30709000	Strong transcription	Fetal Intestine Large	intestine

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