Variant report

Variant	rs3823995
Chromosome Location	chr7:127666089-127666090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127663588..127667936-chr7:127668041..127670204,3	MCF-7	breast:
2	chr7:127659087..127661420-chr7:127663957..127667056,3	K562	blood:
3	chr7:127664155..127666580-chr7:127679902..127682533,2	MCF-7	breast:
4	chr7:127664233..127667371-chr7:127669235..127671920,3	K562	blood:
5	chr7:127663563..127667707-chr7:127669139..127672170,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128594	Chromatin interaction
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1024910	0.82[ASN][1000 genomes]
rs1193333	0.81[ASN][1000 genomes]
rs1193335	0.82[ASN][1000 genomes]
rs1193336	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs124756	0.83[JPT][hapmap]
rs12668077	0.87[JPT][hapmap]
rs1345509	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419968	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes]
rs17732677	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs178734	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2241291	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs225241	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs322813	0.83[JPT][hapmap]
rs322819	0.83[JPT][hapmap]
rs322820	0.83[JPT][hapmap]
rs322821	0.83[JPT][hapmap]
rs322823	0.83[JPT][hapmap]
rs322826	0.93[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs322827	0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs322828	0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs322831	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs322832	0.82[EUR][1000 genomes]
rs322833	0.82[EUR][1000 genomes]
rs322834	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs322835	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs322836	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs322838	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs322840	0.83[JPT][hapmap]
rs35774036	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3757753	0.81[EUR][1000 genomes]
rs3757755	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3757760	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3757763	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3779523	0.83[JPT][hapmap]
rs3779526	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779527	0.81[ASN][1000 genomes]
rs3808056	0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3808061	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808077	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808082	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3808088	0.87[JPT][hapmap]
rs3823994	0.81[AFR][1000 genomes]
rs4731386	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6467155	0.82[ASN][1000 genomes]
rs6467156	0.82[ASN][1000 genomes]
rs6944446	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs6973092	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7789322	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3823995	TMEM209	cis	cerebellum	SCAN
rs3823995	ARF5	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127641600-127670400	Weak transcription	Colonic Mucosa	Colon
2	chr7:127644000-127668800	Weak transcription	Dnd41	blood
3	chr7:127644000-127670200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr7:127644800-127667400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:127644800-127670800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:127645000-127684000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:127645400-127670000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:127651800-127667600	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:127651800-127668800	Weak transcription	Ovary	ovary
10	chr7:127651800-127670600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:127653200-127668800	Weak transcription	Thymus	Thymus
12	chr7:127654600-127669200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:127657000-127670200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:127657800-127669200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr7:127658000-127668800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:127658400-127666600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr7:127658800-127668800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:127658800-127669600	Weak transcription	Stomach Mucosa	stomach
19	chr7:127659000-127667400	Weak transcription	Fetal Kidney	kidney
20	chr7:127660200-127666800	Strong transcription	HepG2	liver
21	chr7:127660400-127667400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:127661000-127667400	Weak transcription	Left Ventricle	heart
23	chr7:127661200-127670400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:127661400-127666400	Weak transcription	Fetal Lung	lung
25	chr7:127661400-127667600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:127661600-127666600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:127661600-127667400	Weak transcription	Gastric	stomach
28	chr7:127661600-127668800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:127661600-127668800	Weak transcription	Pancreas	Pancrea
30	chr7:127661600-127669000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr7:127661600-127670200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:127661600-127670400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:127661800-127666800	Strong transcription	K562	blood
34	chr7:127662200-127669000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr7:127662800-127666600	Enhancers	Brain Cingulate Gyrus	brain
36	chr7:127662800-127668200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr7:127663000-127669200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:127663200-127666200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr7:127663200-127666400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:127663200-127669000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:127663200-127671200	Weak transcription	NHLF	lung
42	chr7:127663200-127671400	Weak transcription	NHDF-Ad	bronchial
43	chr7:127663400-127666600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:127663400-127666800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:127663400-127667400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr7:127663400-127667400	Weak transcription	Esophagus	oesophagus
47	chr7:127663400-127668800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:127663400-127669000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:127663400-127669200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr7:127663400-127669200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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