Variant report

Variant	rs12042829
Chromosome Location	chr1:221896456-221896457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:221895265..221897996-chr1:222013655..222015689,2	K562	blood:
2	chr1:221891993..221895094-chr1:221895705..221898533,3	K562	blood:
3	chr1:221887650..221891571-chr1:221892438..221898117,9	K562	blood:
4	chr1:221895037..221902178-chr1:221912556..221917116,9	K562	blood:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction
ENSG00000227925	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12027098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12030868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12034061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036163	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12041033	1.00[CHB][hapmap];1.00[JPT][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]
rs12044821	1.00[CHB][hapmap];1.00[JPT][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]
rs12116804	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17010269	1.00[EUR][1000 genomes]
rs17010405	1.00[EUR][1000 genomes]
rs4275462	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4846720	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221879600-221902400	Enhancers	Brain Substantia Nigra	brain
2	chr1:221879800-221896800	Enhancers	Colon Smooth Muscle	Colon
3	chr1:221882800-221899000	Genic enhancers	HSMM	muscle
4	chr1:221886600-221897000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:221886600-221897000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:221886600-221897000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:221887200-221899000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:221887800-221898400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:221888000-221899000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:221888000-221903000	Enhancers	Brain Hippocampus Middle	brain
11	chr1:221888600-221896800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:221888800-221898600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:221889000-221896600	Weak transcription	Primary T cells from cord blood	blood
14	chr1:221889400-221899600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:221889800-221899000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:221890400-221898400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:221890600-221896600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:221890800-221906400	Weak transcription	Right Ventricle	heart
19	chr1:221890800-221910200	Weak transcription	Lung	lung
20	chr1:221891800-221911000	Weak transcription	Gastric	stomach
21	chr1:221891800-221913000	Weak transcription	Fetal Intestine Large	intestine
22	chr1:221892200-221898200	Enhancers	HSMMtube	muscle
23	chr1:221892400-221896600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:221892400-221901400	Weak transcription	Small Intestine	intestine
25	chr1:221892600-221898000	Weak transcription	Stomach Mucosa	stomach
26	chr1:221892800-221896800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:221892800-221897000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:221892800-221897400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:221892800-221899000	Weak transcription	Thymus	Thymus
30	chr1:221893000-221896600	Weak transcription	Fetal Lung	lung
31	chr1:221893000-221913600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:221893200-221897000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:221893200-221898000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:221893200-221899400	Genic enhancers	Liver	Liver
35	chr1:221893400-221897000	Weak transcription	Adipose Nuclei	Adipose
36	chr1:221894600-221896600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr1:221894600-221898000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:221894600-221899800	Enhancers	Brain Angular Gyrus	brain
39	chr1:221894800-221896800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:221894800-221896800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:221894800-221897400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:221894800-221897600	Enhancers	K562	blood
43	chr1:221894800-221898600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr1:221894800-221898800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:221895000-221898000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:221895000-221898400	Enhancers	Psoas Muscle	Psoas
47	chr1:221895200-221896800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:221895200-221897000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:221895200-221897600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr1:221895200-221900800	Enhancers	Brain Cingulate Gyrus	brain

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