Variant report

Variant	rs7972201
Chromosome Location	chr12:104884370-104884371
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	chr12:104879669..104882101-chr12:104882975..104884643,2	K562	blood:
2	chr12:104882770..104885599-chr12:104898967..104901298,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11608669	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11609491	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17035663	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1882494	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141855	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2141856	0.89[ASN][1000 genomes]
rs4536299	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs55778791	0.85[ASN][1000 genomes]
rs56020814	0.89[ASN][1000 genomes]
rs56138293	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60351248	0.89[ASN][1000 genomes]
rs7970489	0.85[ASN][1000 genomes]
rs7972097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv868	chr12:104858964-104895572	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1042647	chr12:104861494-104888494	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3338893	chr12:104880122-104884520	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7972201	SYCP3	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104869200-104899600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:104872800-104887000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:104873000-104887600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:104873200-104895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:104875000-104887000	Weak transcription	Placenta	Placenta
6	chr12:104875200-104888000	Weak transcription	HMEC	breast
7	chr12:104875200-104895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:104875200-104897000	Weak transcription	NHEK	skin
9	chr12:104875400-104904200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:104877800-104887000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr12:104878000-104885400	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:104878000-104886000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:104878600-104885000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:104879600-104893200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:104880000-104886800	Enhancers	Fetal Thymus	thymus
16	chr12:104880000-104890800	Weak transcription	Colonic Mucosa	Colon
17	chr12:104880000-104893000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:104880000-104897800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:104880400-104887400	Weak transcription	Esophagus	oesophagus
20	chr12:104880600-104884600	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr12:104880600-104889000	Weak transcription	Fetal Stomach	stomach
22	chr12:104880600-104897000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:104881000-104887000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:104881000-104887200	Weak transcription	Adipose Nuclei	Adipose
25	chr12:104881000-104887800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:104881000-104887800	Weak transcription	HSMM	muscle
27	chr12:104881000-104889600	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:104881200-104887000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:104881200-104890600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:104881400-104887400	Weak transcription	Left Ventricle	heart
31	chr12:104881400-104890000	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:104881600-104898600	Weak transcription	A549	lung
33	chr12:104882200-104887800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:104882600-104885400	Weak transcription	Lung	lung
35	chr12:104882600-104885600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:104882600-104887000	Weak transcription	Brain Anterior Caudate	brain
37	chr12:104882600-104887000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:104882600-104887000	Weak transcription	NHDF-Ad	bronchial
39	chr12:104882600-104887200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:104882600-104888000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:104882600-104888800	Weak transcription	Fetal Lung	lung
42	chr12:104882600-104889800	Weak transcription	Fetal Heart	heart
43	chr12:104882600-104893200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:104882600-104900600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr12:104882800-104887000	Weak transcription	Spleen	Spleen
46	chr12:104883200-104888000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:104883400-104885800	Enhancers	Primary B cells from peripheral blood	blood
48	chr12:104883400-104885800	Enhancers	Primary T cells from cord blood	blood
49	chr12:104883400-104885800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:104883400-104887800	Enhancers	Primary T helper cells PMA-I stimulated	--

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