Variant report

Variant	rs1968029
Chromosome Location	chr13:48628629-48628630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48612034..48614916-chr13:48627197..48628916,2	MCF-7	breast:
2	chr13:48610409..48612253-chr13:48626118..48629626,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136143	Chromatin interaction
ENSG00000136159	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11838539	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12427516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427964	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12428055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428102	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12429099	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429105	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12429348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429993	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12430076	0.85[AMR][1000 genomes]
rs12430172	0.85[AMR][1000 genomes]
rs12431057	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12431130	0.86[EUR][1000 genomes]
rs2094191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148242	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182374	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182375	0.82[ASN][1000 genomes]
rs2182377	0.82[ASN][1000 genomes]
rs2897496	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35710390	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57698455	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57957392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58634823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61585711	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	1.00[JPT][hapmap]
rs8002322	0.82[ASN][1000 genomes]
rs840430	0.82[ASN][1000 genomes]
rs9534910	0.82[ASN][1000 genomes]
rs9534936	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612600-48631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
4	chr13:48612800-48640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:48612800-48640400	Weak transcription	Psoas Muscle	Psoas
6	chr13:48613000-48640200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:48613000-48640400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:48613200-48629000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:48613200-48631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr13:48613200-48640400	Weak transcription	Fetal Heart	heart
11	chr13:48613200-48641600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr13:48613200-48642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:48613400-48641600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr13:48613400-48647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr13:48613600-48636400	Weak transcription	Hela-S3	cervix
16	chr13:48613600-48645000	Weak transcription	Small Intestine	intestine
17	chr13:48614400-48636400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr13:48616400-48642800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:48618800-48644800	Weak transcription	Colonic Mucosa	Colon
20	chr13:48619600-48630200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:48620000-48629000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr13:48620000-48629000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:48620200-48629600	Strong transcription	Fetal Intestine Large	intestine
24	chr13:48620200-48630400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr13:48621000-48629000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr13:48621400-48628800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr13:48621400-48629000	Strong transcription	Liver	Liver
28	chr13:48621600-48628800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr13:48622000-48629000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:48622200-48628800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:48622200-48630400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr13:48622400-48629000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr13:48623200-48640200	Weak transcription	Colon Smooth Muscle	Colon
34	chr13:48623200-48652200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr13:48623400-48630000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr13:48624200-48629000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr13:48624400-48629000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr13:48624800-48629600	Strong transcription	HMEC	breast
39	chr13:48625200-48628800	Strong transcription	Primary B cells from cord blood	blood
40	chr13:48625600-48631400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr13:48625600-48631400	Weak transcription	Fetal Intestine Small	intestine
42	chr13:48625600-48636400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr13:48625600-48640200	Weak transcription	Fetal Kidney	kidney
44	chr13:48625600-48640200	Weak transcription	A549	lung
45	chr13:48625800-48637200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:48625800-48640400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:48626000-48640200	Weak transcription	HUVEC	blood vessel
48	chr13:48626800-48629800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr13:48627200-48639400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr13:48627200-48640200	Weak transcription	NH-A	brain

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