Variant report

Variant	rs10506267
Chromosome Location	chr12:46665836-46665837
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:46665787-46665877	MCF-7	breast:	n/a	n/a
2	POLR2A	chr12:46665809-46665945	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:46665723-46665924	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:46658963-46665919	GM12891	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:46665816-46665866	HCM	heart:	n/a
2	chr12:46665816-46665866	Hela-S3	cervix:	n/a
3	chr12:46665816-46665866	HRCEpiC	kidney:	n/a
4	chr12:46665816-46665866	HRE	kidney:	n/a
5	chr12:46665816-46665866	HCF	heart:	n/a
6	chr12:46665816-46665866	HMEC	breast:	n/a
7	chr12:46665816-46665866	NT2-D1	testis:	n/a
8	chr12:46665816-46665866	HPAEpiC	pulmonary alveolar:	n/a
9	chr12:46665816-46665866	MCF-7	breast:	n/a
10	chr12:46665816-46665866	GM12892	blood:	n/a
11	chr12:46665816-46665866	HAEpiC	amniotic membrane:	n/a
12	chr12:46665816-46665866	GM06990	blood:	n/a
13	chr12:46665816-46665866	HEEpiC	esophagus:	n/a
14	chr12:46665816-46665866	U87	brain:	n/a
15	chr12:46665816-46665866	PFSK-1	brain:	n/a
16	chr12:46665816-46665866	PANC-1	pancreas:	n/a
17	chr12:46665816-46665866	NH-A	brain:	n/a
18	chr12:46665816-46665866	IMR90	lung:	fetal
19	chr12:46665816-46665866	SAEC	small airway:	n/a
20	chr12:46665816-46665866	NHDF-neo	bronchial:	n/a
21	chr12:46665816-46665866	SK-N-SH_RA	brain:	n/a
22	chr12:46665816-46665866	Hepatocyte	liver:	n/a
23	chr12:46665816-46665866	Jurkat	blood:	n/a
24	chr12:46665816-46665866	LNCaP	prostate:	n/a
25	chr12:46665816-46665866	GM12878	blood:	n/a
26	chr12:46665816-46665866	HL-60	blood:	n/a
27	chr12:46665816-46665866	GM19239	blood:	n/a
28	chr12:46665816-46665866	AoSMC	blood vessel:	n/a
29	chr12:46665816-46665866	BE2_C	brain:	n/a
30	chr12:46665816-46665866	HNPCEpiC	eye:	n/a
31	chr12:46665816-46665866	A549	lung:	n/a
32	chr12:46665816-46665866	Caco-2	colon:	n/a
33	chr12:46665816-46665866	HepG2	liver:	n/a
34	chr12:46665816-46665866	HIPEpiC	eye:	n/a
35	chr12:46665816-46665866	RPTEC	kidney:	n/a
36	chr12:46665816-46665866	T-47D	breast:	n/a
37	chr12:46665816-46665866	HCT-116	colon:	n/a
38	chr12:46665816-46665866	SKMC	muscle:	n/a
39	chr12:46665816-46665866	AG04449	skin:	fetal
40	chr12:46665816-46665866	GM12891	blood:	n/a
41	chr12:46665816-46665866	AG09319	gingival:	n/a
42	chr12:46665816-46665866	ECC-1	luminal epithelium:	n/a
43	chr12:46665816-46665866	NB4	blood:	n/a
44	chr12:46665816-46665866	HRPEpiC	eye:	n/a
45	chr12:46665816-46665866	NHBE	bronchial:	n/a
46	chr12:46665816-46665866	ProgFib	skin:	n/a
47	chr12:46665816-46665866	CMK	blood:	n/a
48	chr12:46665816-46665866	K562	blood:	n/a
49	chr12:46665816-46665866	AG09309	skin:	n/a
50	chr12:46665816-46665866	BJ	skin:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46664868..46666420-chr12:46696622..46698481,2	MCF-7	breast:
2	chr12:46562964..46565138-chr12:46663936..46666612,3	MCF-7	breast:
3	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
4	chr12:46663312..46666406-chr12:46754623..46758323,3	K562	blood:
5	chr12:46665546..46668026-chr12:46755875..46758444,2	MCF-7	breast:
6	chr12:46664274..46666406-chr12:46754623..46757460,2	K562	blood:

No data

Variant related genes	Relation type
SLC38A1	TF binding region
SLC38A1	CpG island
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10506268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183454	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs11183467	0.83[CHB][hapmap]
rs11183482	0.83[CHB][hapmap]
rs1125908	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs11830769	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11831535	0.91[AMR][1000 genomes]
rs11834905	1.00[EUR][1000 genomes]
rs12299499	0.93[CHB][hapmap]
rs12317255	0.83[CHB][hapmap]
rs13377959	0.83[CHB][hapmap]
rs17096884	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs17096922	0.83[CHB][hapmap]
rs2125646	0.89[CHB][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2307062	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs2307063	0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs2408509	0.89[CHB][hapmap];1.00[EUR][1000 genomes]
rs3742061	0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs3843676	0.91[AMR][1000 genomes]
rs56222195	1.00[EUR][1000 genomes]
rs57067899	1.00[EUR][1000 genomes]
rs57149475	1.00[EUR][1000 genomes]
rs57271454	1.00[EUR][1000 genomes]
rs57425661	1.00[EUR][1000 genomes]
rs58470507	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59702903	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs60628240	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60977966	1.00[EUR][1000 genomes]
rs61232019	1.00[EUR][1000 genomes]
rs61406609	1.00[EUR][1000 genomes]
rs61517444	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73282532	1.00[EUR][1000 genomes]
rs73282561	1.00[EUR][1000 genomes]
rs73282591	1.00[EUR][1000 genomes]
rs74082085	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs74083707	1.00[EUR][1000 genomes]
rs74083710	1.00[EUR][1000 genomes]
rs74084031	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954314	0.83[CHB][hapmap]
rs7967889	0.84[CHB][hapmap]
rs923788	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46664000-46675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:46664200-46677400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:46664400-46666000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr12:46664400-46666000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr12:46664400-46666400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:46664400-46666600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:46664400-46673800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:46664600-46666800	Enhancers	Primary T cells from cord blood	blood
9	chr12:46664600-46667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:46664600-46667200	Weak transcription	Fetal Intestine Small	intestine
11	chr12:46664800-46670000	Weak transcription	Primary B cells from cord blood	blood
12	chr12:46664800-46671800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:46665000-46666000	Enhancers	Fetal Thymus	thymus
14	chr12:46665000-46666200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:46665000-46667600	Enhancers	Fetal Muscle Leg	muscle
16	chr12:46665200-46670600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:46665200-46671600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:46665200-46673200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:46665200-46673400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:46665200-46677200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:46665400-46666000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:46665400-46667600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr12:46665400-46670400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:46665400-46674000	Weak transcription	GM12878-XiMat	blood
25	chr12:46665400-46676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:46665600-46666000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:46665600-46666000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:46665600-46672800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:46665600-46675600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:46665800-46666000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:46665800-46666000	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links