Variant report

Variant	rs12126599
Chromosome Location	chr1:171467731-171467732
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	chr1:171465551..171468754-chr1:171477874..171481569,3	K562	blood:
2	chr1:171452836..171454712-chr1:171467319..171469228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117523	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10913129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12124034	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12126218	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12134052	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12136219	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12145006	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12145591	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12146098	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12403390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387832	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17586576	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17646340	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6425276	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12126599	KLHL20	cis	parietal	SCAN
rs12126599	TNFSF18	cis	parietal	SCAN
rs12126599	DNM3	cis	cerebellum	SCAN
rs12126599	BRP44	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171455800-171467800	Weak transcription	Spleen	Spleen
2	chr1:171456000-171481800	Weak transcription	Placenta	Placenta
3	chr1:171456200-171467800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:171456200-171475000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:171456400-171467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:171456400-171468400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:171456400-171470200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:171456400-171471200	Weak transcription	Thymus	Thymus
9	chr1:171456400-171473000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:171456400-171481800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:171456400-171483600	Weak transcription	Fetal Intestine Large	intestine
12	chr1:171456600-171469600	Weak transcription	Fetal Stomach	stomach
13	chr1:171456800-171474800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:171457200-171469000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:171457600-171471000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:171457800-171482000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:171457800-171482200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:171458200-171471000	Weak transcription	Fetal Brain Female	brain
19	chr1:171459000-171482000	Weak transcription	HMEC	breast
20	chr1:171460400-171471800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:171460800-171468000	Weak transcription	Dnd41	blood
22	chr1:171460800-171470200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:171460800-171470600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:171460800-171481400	Weak transcription	HSMM	muscle
25	chr1:171461800-171468200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr1:171461800-171469800	Weak transcription	Primary B cells from cord blood	blood
27	chr1:171461800-171470400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:171462200-171468400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:171462600-171467800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:171462600-171468800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:171462600-171471200	Weak transcription	Right Atrium	heart
32	chr1:171462600-171478000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:171462600-171482400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:171462800-171469200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:171463000-171483200	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:171464000-171475200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:171464000-171483200	Weak transcription	Esophagus	oesophagus
38	chr1:171464200-171467800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr1:171464200-171471000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:171464200-171474600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:171464200-171476000	Weak transcription	NHDF-Ad	bronchial
42	chr1:171464200-171476800	Weak transcription	Brain Angular Gyrus	brain
43	chr1:171464200-171481600	Weak transcription	NHEK	skin
44	chr1:171464400-171469600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:171464400-171470000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:171464400-171470600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:171464400-171470600	Weak transcription	Fetal Brain Male	brain
48	chr1:171464400-171475400	Weak transcription	NH-A	brain
49	chr1:171464600-171468000	Weak transcription	Primary T cells from cord blood	blood
50	chr1:171464600-171468000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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