Variant report

Variant	rs61588443
Chromosome Location	chr3:196013318-196013319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196012776..196015922-chr3:196063347..196066816,3	MCF-7	breast:
2	chr3:196012377..196016502-chr3:196041586..196047553,11	K562	blood:
3	chr3:195965458..195967733-chr3:196012588..196015404,2	MCF-7	breast:
4	chr3:196012669..196015162-chr3:196043820..196046764,2	K562	blood:
5	chr3:196010976..196013330-chr3:196068543..196070894,2	MCF-7	breast:
6	chr3:196012352..196016755-chr3:196062622..196069148,9	K562	blood:
7	chr3:196012576..196016636-chr3:196061383..196069148,11	K562	blood:

Variant related genes	Relation type
ENSG00000212146	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000161217	Chromatin interaction
ENSG00000272741	Chromatin interaction
ENSG00000273331	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000235897	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12632779	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12633454	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12633827	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12634350	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12634587	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12635925	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1357290	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772107	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772108	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4396926	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4916484	0.84[ASN][1000 genomes]
rs56701784	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57987393	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58297632	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58568267	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58845625	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59289255	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59708858	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60167422	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61254593	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66935510	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67199839	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72611187	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72611188	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72611189	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72611190	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73212156	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73212176	0.80[ASN][1000 genomes]
rs7617236	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7635355	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
18	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
19	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61588443	TCTEX1D2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196000600-196013800	Weak transcription	Aorta	Aorta
2	chr3:196001000-196013800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:196001200-196013600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:196006600-196013600	Weak transcription	Lung	lung
5	chr3:196006600-196013800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:196007200-196013800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:196007400-196013800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:196010000-196013800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:196010400-196013800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:196010400-196013800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:196010600-196013400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:196011200-196013400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:196011400-196013800	Enhancers	Placenta	Placenta
14	chr3:196011600-196013800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:196011600-196013800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr3:196011600-196013800	Enhancers	Thymus	Thymus
17	chr3:196011800-196013400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:196012000-196013600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:196012000-196013800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:196012000-196014000	Enhancers	Spleen	Spleen
21	chr3:196012200-196013600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:196012200-196013800	Enhancers	Primary hematopoietic stem cells	blood
23	chr3:196012400-196013400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:196012400-196013400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr3:196012400-196013400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:196012400-196013400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:196012400-196013400	Flanking Active TSS	K562	blood
28	chr3:196012400-196013400	Flanking Active TSS	NHDF-Ad	bronchial
29	chr3:196012400-196013600	Flanking Active TSS	Hela-S3	cervix
30	chr3:196012400-196013600	Flanking Active TSS	Osteobl	bone
31	chr3:196012400-196013800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr3:196012400-196013800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr3:196012400-196013800	Enhancers	Fetal Brain Male	brain
34	chr3:196012400-196013800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr3:196012400-196014000	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr3:196012400-196014000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr3:196012400-196014200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:196012400-196014200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr3:196012400-196014400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr3:196012400-196014800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr3:196012400-196015400	Active TSS	Rectal Smooth Muscle	rectum
42	chr3:196012400-196015600	Active TSS	HSMMtube	muscle
43	chr3:196012600-196013400	Enhancers	Brain Hippocampus Middle	brain
44	chr3:196012600-196013400	Flanking Active TSS	Fetal Heart	heart
45	chr3:196012600-196013400	Flanking Active TSS	HMEC	breast
46	chr3:196012600-196013600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr3:196012600-196013600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr3:196012600-196013600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:196012600-196013600	Enhancers	Brain Substantia Nigra	brain
50	chr3:196012600-196013600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links