Variant report

Variant	rs4512653
Chromosome Location	chr1:9815543-9815544
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr1:9815435-9815797	T-47D	breast:	n/a	n/a
2	FOXA1	chr1:9815433-9815753	T-47D	breast:	n/a	n/a
3	FOXA2	chr1:9815453-9815712	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9815045..9817854-chr1:9822064..9824472,2	K562	blood:

Variant related genes	Relation type
CLSTN1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10779730	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10864436	0.88[CHB][hapmap]
rs10864437	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10864438	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11121484	0.87[AMR][1000 genomes]
rs11121485	0.84[EUR][1000 genomes]
rs11121486	0.88[CHB][hapmap];0.84[EUR][1000 genomes]
rs11121488	0.84[EUR][1000 genomes]
rs11121489	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121490	0.95[ASN][1000 genomes]
rs11121492	0.88[CHB][hapmap]
rs11674	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11804356	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806520	0.90[ASN][1000 genomes]
rs12021914	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12037599	0.88[CHB][hapmap]
rs12042293	0.88[CHB][hapmap];0.84[EUR][1000 genomes]
rs12047054	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12064975	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088273	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1220419	0.82[ASN][1000 genomes]
rs12568720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12569008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1615629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1660741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1660742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17034335	0.88[CHB][hapmap]
rs4845975	0.82[ASN][1000 genomes]
rs56109009	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6666296	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs6677664	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs72855716	0.96[ASN][1000 genomes]
rs7526958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550246	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7550295	0.88[CHB][hapmap]
rs767762	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9784200-9815800	Strong transcription	Fetal Intestine Small	intestine
2	chr1:9789800-9815800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:9791600-9816000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:9792000-9815600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:9794000-9815600	Strong transcription	Fetal Stomach	stomach
6	chr1:9794200-9815600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:9794200-9815800	Strong transcription	Thymus	Thymus
8	chr1:9798200-9815600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:9798200-9816000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:9798600-9815600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:9799400-9815600	Strong transcription	Dnd41	blood
12	chr1:9800600-9821600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:9801000-9815800	Weak transcription	Psoas Muscle	Psoas
14	chr1:9801200-9837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:9801400-9854200	Weak transcription	Fetal Kidney	kidney
16	chr1:9804400-9836600	Weak transcription	Small Intestine	intestine
17	chr1:9804600-9836600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:9804800-9815600	Weak transcription	HUVEC	blood vessel
19	chr1:9806000-9815600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:9806400-9825800	Weak transcription	HSMMtube	muscle
21	chr1:9806800-9819000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:9807600-9816200	Strong transcription	Primary T cells from cord blood	blood
23	chr1:9808000-9815600	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:9808200-9815600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:9808400-9815800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:9810000-9815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:9810000-9832400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:9810200-9816000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:9810200-9825800	Weak transcription	NHDF-Ad	bronchial
30	chr1:9810200-9826000	Weak transcription	Hela-S3	cervix
31	chr1:9810200-9826000	Weak transcription	HSMM	muscle
32	chr1:9810200-9829200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:9810400-9825800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:9811600-9832400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:9811600-9832400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:9811800-9818800	Weak transcription	NHLF	lung
37	chr1:9811800-9819600	Weak transcription	Liver	Liver
38	chr1:9811800-9832400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:9811800-9857000	Weak transcription	Aorta	Aorta
40	chr1:9812000-9826200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:9812200-9820000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:9812400-9816400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:9812400-9832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:9812600-9818800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:9812600-9829000	Weak transcription	Stomach Mucosa	stomach
46	chr1:9812800-9831000	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:9813400-9819000	Weak transcription	Placenta	Placenta
48	chr1:9813400-9819800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:9813400-9829000	Weak transcription	Colonic Mucosa	Colon
50	chr1:9813400-9830400	Weak transcription	GM12878-XiMat	blood

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