Variant report

Variant	rs2645029
Chromosome Location	chr11:9812236-9812237
allele	A/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	GATA1	chr11:9811196-9812483	PBDE	blood:	n/a	chr11:9812305-9812314 chr11:9811686-9811694 chr11:9812296-9812313 chr11:9812305-9812315
2	GATA1	chr11:9811275-9813817	K562	blood:	n/a	chr11:9812305-9812314 chr11:9811686-9811694 chr11:9812296-9812313 chr11:9812305-9812315
3	ARID3A	chr11:9812132-9812964	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9805616..9807333-chr11:9812075..9813772,2	K562	blood:

Variant related genes	Relation type
SBF2	TF binding region
ENSG00000133812	Chromatin interaction
ENSG00000246273	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10118	0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10770062	0.89[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs1392026	0.93[ASN][1000 genomes]
rs183110	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1875030	0.91[ASN][1000 genomes]
rs2173030	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645017	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs360120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360124	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360127	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360129	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360131	0.99[ASN][1000 genomes]
rs360132	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360140	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs360141	0.92[ASN][1000 genomes]
rs360142	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360146	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360158	0.94[CHB][hapmap]
rs380806	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs391304	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs394315	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs432849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs438151	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs446760	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs472487	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs634680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6483726	0.84[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2645029	PPFIBP2	cis	cerebellum	SCAN
rs2645029	MRPL17	cis	cerebellum	SCAN
rs2645029	CNGA4	cis	parietal	SCAN
rs2645029	CSNK2A1P	cis	parietal	SCAN
rs2645029	C11orf17	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9780600-9813200	Weak transcription	Small Intestine	intestine
2	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:9797400-9821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr11:9799600-9823400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:9799800-9814200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:9800200-9823800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:9801600-9823800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:9803000-9823400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:9803000-9823400	Weak transcription	Psoas Muscle	Psoas
10	chr11:9803200-9828600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:9803200-9828600	Weak transcription	Gastric	stomach
12	chr11:9803200-9828800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr11:9805000-9812800	Strong transcription	HepG2	liver
14	chr11:9805000-9815600	Strong transcription	Fetal Intestine Large	intestine
15	chr11:9805200-9815600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:9806800-9821400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:9806800-9828600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:9807200-9823200	Weak transcription	Fetal Heart	heart
19	chr11:9808400-9828800	Weak transcription	Fetal Kidney	kidney
20	chr11:9808800-9812600	Genic enhancers	NHDF-Ad	bronchial
21	chr11:9809600-9823000	Weak transcription	HMEC	breast
22	chr11:9809600-9828600	Weak transcription	Esophagus	oesophagus
23	chr11:9809600-9832600	Weak transcription	Colonic Mucosa	Colon
24	chr11:9809800-9813200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr11:9809800-9813800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:9809800-9819800	Weak transcription	Pancreas	Pancrea
27	chr11:9809800-9823200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:9809800-9828000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr11:9809800-9828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:9810000-9818400	Weak transcription	Aorta	Aorta
31	chr11:9810000-9822400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:9810000-9823200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr11:9810000-9823200	Weak transcription	NH-A	brain
34	chr11:9810000-9829200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr11:9810200-9812400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:9810200-9819800	Weak transcription	Hela-S3	cervix
37	chr11:9810200-9821000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:9810200-9822600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:9810200-9828400	Weak transcription	Primary T cells from cord blood	blood
40	chr11:9810200-9829200	Weak transcription	Fetal Brain Male	brain
41	chr11:9810400-9814000	Weak transcription	A549	lung
42	chr11:9810600-9812400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:9810600-9812400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:9810600-9816000	Strong transcription	HSMMtube	muscle
45	chr11:9810800-9812400	Enhancers	K562	blood
46	chr11:9810800-9812600	Strong transcription	Osteobl	bone
47	chr11:9810800-9813200	Strong transcription	HSMM	muscle
48	chr11:9810800-9815200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr11:9810800-9818200	Weak transcription	Spleen	Spleen
50	chr11:9810800-9820800	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links