Variant report

Variant	rs3095327
Chromosome Location	chr6:30699022-30699023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30646332..30647297-chr6:30698013..30699287,6	MCF-7	breast:
2	chr6:30614002..30615916-chr6:30697088..30699807,3	MCF-7	breast:
3	chr6:30696761..30700438-chr6:30779538..30781456,3	K562	blood:
4	chr6:30565122..30567230-chr6:30697537..30699633,2	MCF-7	breast:
5	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
6	chr22:29205328..29207798-chr6:30697845..30700458,2	MCF-7	breast:
7	chr6:30640427..30641170-chr6:30698319..30699252,3	K562	blood:
8	chr6:30646486..30647794-chr6:30698350..30699317,4	K562	blood:
9	chr6:30646692..30647419-chr6:30698658..30699269,4	MCF-7	breast:
10	chr6:30696071..30700958-chr6:30848494..30852857,5	MCF-7	breast:
11	chr6:30580720..30584703-chr6:30697012..30700631,3	MCF-7	breast:
12	chr6:30697464..30700197-chr6:30850682..30852758,2	MCF-7	breast:
13	chr6:30698701..30700492-chr6:30786748..30789246,2	MCF-7	breast:
14	chr6:30697310..30700466-chr6:30842100..30845469,3	K562	blood:
15	chr6:30642470..30648471-chr6:30697241..30700740,8	MCF-7	breast:
16	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:
17	chr6:30614277..30616779-chr6:30698677..30700989,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000266183	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1059612	0.91[EUR][1000 genomes]
rs3094125	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3095326	0.81[EUR][1000 genomes]
rs3095328	0.82[EUR][1000 genomes]
rs3095332	0.82[EUR][1000 genomes]
rs3129972	0.83[EUR][1000 genomes]
rs3129973	0.81[EUR][1000 genomes]
rs3129974	0.82[EUR][1000 genomes]
rs3130658	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130660	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132582	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132583	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132585	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132600	0.81[EUR][1000 genomes]
rs9262126	0.88[EUR][1000 genomes]
rs9262130	0.88[EUR][1000 genomes]
rs9262132	0.88[EUR][1000 genomes]
rs9262135	0.88[EUR][1000 genomes]
rs9262141	0.85[EUR][1000 genomes]
rs9262142	0.85[EUR][1000 genomes]
rs9262143	0.85[EUR][1000 genomes]
rs9262146	0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3095327	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3095327	TUBB	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	chr6:30690200-30699200	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:30690400-30709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:30690600-30701200	Strong transcription	Brain Angular Gyrus	brain
5	chr6:30690600-30703800	Strong transcription	Lung	lung
6	chr6:30691000-30703800	Strong transcription	Brain Cingulate Gyrus	brain
7	chr6:30692600-30708200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:30693200-30708800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:30693400-30709000	Strong transcription	Fetal Stomach	stomach
10	chr6:30693800-30704200	Strong transcription	Fetal Lung	lung
11	chr6:30693800-30709000	Strong transcription	Fetal Brain Female	brain
12	chr6:30694000-30708800	Weak transcription	Fetal Brain Male	brain
13	chr6:30694200-30705600	Weak transcription	Small Intestine	intestine
14	chr6:30694400-30707800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:30694600-30704800	Weak transcription	Right Atrium	heart
16	chr6:30694800-30699200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:30695400-30708200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:30695400-30709000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:30695400-30709200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:30695600-30699200	Strong transcription	Ovary	ovary
21	chr6:30695600-30707800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:30696200-30707400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:30696400-30709000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:30696600-30706800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:30696800-30705600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:30696800-30707400	Strong transcription	NHLF	lung
27	chr6:30697000-30707600	Strong transcription	Osteobl	bone
28	chr6:30697000-30707800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:30697000-30708600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:30697000-30709200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:30697200-30699800	Strong transcription	A549	lung
32	chr6:30697200-30700200	Strong transcription	Dnd41	blood
33	chr6:30697200-30700600	Strong transcription	Aorta	Aorta
34	chr6:30697200-30700800	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr6:30697200-30700800	Strong transcription	Hela-S3	cervix
36	chr6:30697400-30700800	Strong transcription	HSMMtube	muscle
37	chr6:30697600-30699400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr6:30697600-30699600	Genic enhancers	HepG2	liver
39	chr6:30697800-30699600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr6:30697800-30705800	Weak transcription	NH-A	brain
41	chr6:30698000-30699400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:30698000-30699600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:30698200-30700200	Weak transcription	Brain Substantia Nigra	brain
44	chr6:30698200-30700600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr6:30698200-30705200	Weak transcription	Fetal Kidney	kidney
46	chr6:30698400-30699200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr6:30698400-30700400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr6:30698400-30701200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:30698400-30703000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:30698400-30703800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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