Variant report

Variant	rs12189857
Chromosome Location	chr6:101303798-101303799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:101302214..101305047-chr6:101327915..101330416,2	MCF-7	breast:
2	chr6:101298656..101300924-chr6:101302449..101304215,2	MCF-7	breast:
3	chr6:101302750..101305984-chr6:101307403..101310104,4	K562	blood:
4	chr6:101302750..101305645-chr6:101307403..101308925,2	K562	blood:

Variant related genes	Relation type
ENSG00000112249	Chromatin interaction
ENSG00000260000	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11155726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061209	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061230	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17673031	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2749130	1.00[ASN][1000 genomes]
rs2756040	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895068	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs592463	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600653	1.00[ASN][1000 genomes]
rs601360	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606032	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609522	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612117	1.00[ASN][1000 genomes]
rs612459	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613338	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614097	1.00[ASN][1000 genomes]
rs617365	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625745	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626411	1.00[ASN][1000 genomes]
rs635258	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640315	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648360	0.82[EUR][1000 genomes]
rs668932	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673138	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674589	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705594	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705595	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705598	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705601	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705602	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705609	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705612	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705618	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705619	0.81[EUR][1000 genomes]
rs72944877	1.00[ASN][1000 genomes]
rs72946427	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947091	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951137	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951161	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755696	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs817226	1.00[ASN][1000 genomes]
rs817227	1.00[ASN][1000 genomes]
rs817234	1.00[ASN][1000 genomes]
rs846784	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846790	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846796	0.82[EUR][1000 genomes]
rs861752	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1016353	chr6:101172705-101304041	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
9	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12189857	ASCC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101184400-101304600	Weak transcription	Hela-S3	cervix
2	chr6:101215200-101311400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:101233600-101306600	Weak transcription	K562	blood
4	chr6:101253400-101304200	Weak transcription	Primary T cells from cord blood	blood
5	chr6:101269200-101326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:101275800-101314400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:101278000-101306600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:101278000-101313800	Weak transcription	Fetal Intestine Small	intestine
9	chr6:101281200-101317000	Weak transcription	Small Intestine	intestine
10	chr6:101282000-101311400	Weak transcription	Aorta	Aorta
11	chr6:101284800-101304000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:101285000-101304400	Weak transcription	Brain Substantia Nigra	brain
13	chr6:101285600-101326600	Weak transcription	NHLF	lung
14	chr6:101287800-101313000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:101289200-101304800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:101289800-101304400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:101290200-101304200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:101290200-101306600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:101290200-101318200	Weak transcription	Fetal Lung	lung
20	chr6:101290600-101312800	Weak transcription	Fetal Brain Male	brain
21	chr6:101290800-101311400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:101290800-101311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:101291200-101326400	Weak transcription	Brain Anterior Caudate	brain
24	chr6:101291400-101314000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:101291600-101314000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:101291800-101312800	Weak transcription	Gastric	stomach
27	chr6:101292600-101310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:101294000-101320400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:101294200-101314200	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:101294600-101307000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:101294600-101310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:101294600-101311400	Weak transcription	Pancreas	Pancrea
33	chr6:101294600-101314400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:101294600-101320600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:101294600-101325400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr6:101294600-101328600	Weak transcription	Spleen	Spleen
37	chr6:101294800-101325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:101295000-101325800	Weak transcription	Brain Angular Gyrus	brain
39	chr6:101295000-101325800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:101295800-101305000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:101296000-101323400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:101296200-101306800	Weak transcription	HUVEC	blood vessel
43	chr6:101296600-101303800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:101296600-101303800	Weak transcription	HMEC	breast
45	chr6:101296600-101304000	Weak transcription	Primary B cells from cord blood	blood
46	chr6:101296600-101304000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr6:101296600-101304400	Weak transcription	Placenta	Placenta
48	chr6:101296600-101306800	Weak transcription	HepG2	liver
49	chr6:101296600-101310000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:101296800-101304600	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links