Variant report

Variant	rs3129996
Chromosome Location	chr6:30651587-30651588
allele	A/C
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30651552..30657864-chr6:30708721..30713716,15	MCF-7	breast:
2	chr12:6539489..6539998-chr6:30650974..30651701,2	Hela-S3	cervix:
3	chr6:30651503..30654024-chr6:30850794..30852949,2	MCF-7	breast:
4	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
5	chr6:30649806..30652040-chr6:30852891..30855625,2	MCF-7	breast:
6	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
7	chr6:30650251..30652093-chr6:30710839..30712896,2	MCF-7	breast:
8	chr6:30580498..30587281-chr6:30649167..30662031,51	K562	blood:
9	chr6:30648927..30651629-chr6:30742930..30745365,2	K562	blood:
10	chr6:30650916..30653194-chr6:30673902..30676793,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204568	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137337	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs3094092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094124	0.82[EUR][1000 genomes]
rs3130000	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130040	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3130245	0.93[AMR][1000 genomes]
rs3132587	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3132611	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9262081	0.96[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
6	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
7	nsv884094	chr6:30637998-30660611	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv884095	chr6:30644987-30664567	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv884096	chr6:30647979-30664567	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv884097	chr6:30650378-30660611	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
13	nsv884098	chr6:30650378-30664567	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3129996	HCG22	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30644200-30653800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:30645000-30651800	Weak transcription	Ovary	ovary
3	chr6:30646600-30653400	Transcr. at gene 5' and 3'	NHLF	lung
4	chr6:30646600-30653800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:30646800-30653200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:30646800-30653600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:30646800-30653800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:30647000-30651600	Transcr. at gene 5' and 3'	Osteobl	bone
9	chr6:30647000-30653400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
10	chr6:30647000-30653800	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr6:30647400-30653600	Transcr. at gene 5' and 3'	NHEK	skin
12	chr6:30648400-30654400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:30648600-30655600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:30648800-30651600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:30649000-30653800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
16	chr6:30649000-30656200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:30649200-30652200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr6:30649200-30652800	Active TSS	HSMMtube	muscle
19	chr6:30649200-30654000	Active TSS	Brain Hippocampus Middle	brain
20	chr6:30649200-30654400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr6:30649200-30655200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr6:30649400-30651800	Flanking Active TSS	Hela-S3	cervix
23	chr6:30649400-30652200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr6:30649400-30653800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
25	chr6:30649400-30656000	Active TSS	Aorta	Aorta
26	chr6:30649600-30651600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:30649600-30652200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:30649600-30652400	Flanking Active TSS	Liver	Liver
29	chr6:30649600-30653000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:30649600-30653800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
31	chr6:30649600-30653800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:30649600-30655400	Active TSS	Gastric	stomach
33	chr6:30649600-30655800	Active TSS	Brain Cingulate Gyrus	brain
34	chr6:30649600-30656000	Active TSS	Lung	lung
35	chr6:30649600-30656000	Active TSS	Small Intestine	intestine
36	chr6:30649800-30651600	Flanking Active TSS	A549	lung
37	chr6:30649800-30652400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr6:30649800-30652400	Flanking Active TSS	Placenta	Placenta
39	chr6:30649800-30653400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:30649800-30655400	Active TSS	Primary T cells from cord blood	blood
41	chr6:30649800-30655600	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr6:30650000-30651600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr6:30650000-30651600	Flanking Active TSS	Right Ventricle	heart
44	chr6:30650000-30652400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:30650000-30653600	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
46	chr6:30650000-30653800	Active TSS	Brain Substantia Nigra	brain
47	chr6:30650000-30653800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
48	chr6:30650000-30655400	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr6:30650000-30655600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:30650000-30656200	Active TSS	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links