Variant report

Variant	rs41291961
Chromosome Location	chr12:48526892-48526893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48520102..48522830-chr12:48525176..48527649,3	MCF-7	breast:
2	chr12:48499471..48501455-chr12:48525096..48527128,3	MCF-7	breast:
3	chr12:48523386..48526206-chr12:48526341..48529296,3	K562	blood:
4	chr12:48518849..48522822-chr12:48523598..48527122,4	K562	blood:
5	chr12:48514233..48517201-chr12:48525385..48527405,2	K562	blood:
6	chr12:48525679..48529309-chr12:48532044..48535896,3	K562	blood:
7	chr12:48524575..48527145-chr12:48529433..48531470,2	K562	blood:

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1004746	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1004806	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10506277	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12301562	0.83[EUR][1000 genomes]
rs17224674	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17225261	0.89[AMR][1000 genomes]
rs17225366	0.89[AMR][1000 genomes]
rs17225751	0.89[AMR][1000 genomes]
rs17607800	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17824200	0.89[AMR][1000 genomes]
rs2228501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3936179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4075914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41291959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55682541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55707383	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs55752728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55794326	0.89[AMR][1000 genomes]
rs55886138	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55890195	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55894137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55945889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55953382	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56049209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56116946	0.89[AMR][1000 genomes]
rs56187356	0.93[EUR][1000 genomes]
rs56205628	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56288528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56378908	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60209369	0.83[EUR][1000 genomes]
rs74089155	0.93[EUR][1000 genomes]
rs74089159	0.82[EUR][1000 genomes]
rs74089163	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers 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 miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41291961	ZNF641	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48513600-48527000	Weak transcription	Pancreas	Pancrea
2	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:48514200-48527000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:48516200-48529600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:48516400-48529400	Strong transcription	Ovary	ovary
12	chr12:48516400-48529600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:48516400-48535600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:48516400-48535800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:48516400-48542000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:48516400-48545000	Strong transcription	GM12878-XiMat	blood
17	chr12:48516400-48545400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:48516400-48545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
22	chr12:48516600-48527800	Weak transcription	Small Intestine	intestine
23	chr12:48516600-48536600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:48516600-48543200	Weak transcription	Stomach Mucosa	stomach
25	chr12:48516600-48545400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:48516600-48545600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:48516800-48529400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:48516800-48530400	Strong transcription	Osteobl	bone
29	chr12:48516800-48547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:48517200-48529600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:48517600-48547400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:48518200-48529800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr12:48518600-48547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:48519000-48527800	Weak transcription	Fetal Thymus	thymus
35	chr12:48519600-48547200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:48519800-48529800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:48520000-48529400	Strong transcription	NHEK	skin
38	chr12:48520000-48545600	Strong transcription	Hela-S3	cervix
39	chr12:48520600-48529400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:48520600-48529600	Strong transcription	HSMM	muscle
41	chr12:48520600-48529800	Strong transcription	Brain Germinal Matrix	brain
42	chr12:48520800-48547400	Strong transcription	Fetal Brain Female	brain
43	chr12:48521000-48529400	Strong transcription	Brain Anterior Caudate	brain
44	chr12:48521400-48529600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr12:48522000-48529400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:48522400-48534400	Weak transcription	NHDF-Ad	bronchial
47	chr12:48522600-48529400	Strong transcription	Aorta	Aorta
48	chr12:48522600-48529600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr12:48522600-48532800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:48522800-48530200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links