Variant report

Variant	rs11211346
Chromosome Location	chr1:47185776-47185777
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	ELF1	chr1:47185466-47185931	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:47183189-47185848	Hela-S3	cervix:	n/a	n/a
3	SP1	chr1:47184319-47185840	HCT-116	colon:	n/a	chr1:47184883-47184894 chr1:47184509-47184521 chr1:47184948-47184957 chr1:47184511-47184520 chr1:47184509-47184521 chr1:47185021-47185030 chr1:47184880-47184894 chr1:47184947-47184959 chr1:47184947-47184959 chr1:47184949-47184958 chr1:47184948-47184958 chr1:47184918-47184927 chr1:47184510-47184519 chr1:47184948-47184958 chr1:47184822-47184843 chr1:47184948-47184962 chr1:47184898-47184905 chr1:47184948-47184957 chr1:47185078-47185088
4	ATF1	chr1:47185343-47185785	K562	blood:	n/a	n/a
5	CEBPD	chr1:47184325-47185795	K562	blood:	n/a	n/a
6	NR2F2	chr1:47185325-47185820	MCF-7	breast:	n/a	n/a
7	JUND	chr1:47184586-47185822	K562	blood:	n/a	chr1:47184831-47184840 chr1:47184852-47184861
8	ELF1	chr1:47185491-47185850	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr1:47184306-47185972	MCF-7	breast:	n/a	n/a
10	CBX3	chr1:47184415-47185836	K562	blood:	n/a	n/a
11	KAP1	chr1:47184786-47185785	U2OS	brain:	n/a	n/a
12	GATA3	chr1:47185230-47185898	MCF-7	breast:	n/a	chr1:47185619-47185626 chr1:47185461-47185469
13	RCOR1	chr1:47184456-47185839	K562	blood:	n/a	n/a
14	TBP	chr1:47184682-47185823	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:47185463-47185780	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr1:47184665-47185809	Hela-S3	cervix:	n/a	n/a
17	USF2	chr1:47184981-47185819	Hela-S3	cervix:	n/a	n/a
18	HCFC1	chr1:47184169-47185884	Hela-S3	cervix:	n/a	n/a
19	GATA3	chr1:47185228-47185795	MCF-7	breast:	n/a	chr1:47185619-47185626 chr1:47185461-47185469
20	MXI1	chr1:47184030-47185896	SK-N-SH	brain:	n/a	n/a
21	JUN	chr1:47183215-47186038	K562	blood:	n/a	chr1:47184831-47184840 chr1:47184852-47184861 chr1:47184848-47184861 chr1:47184512-47184521
22	ELF1	chr1:47185432-47185826	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47134358..47137339-chr1:47183387..47185827,2	MCF-7	breast:
2	chr1:47133847..47136859-chr1:47183270..47186412,3	K562	blood:
3	chr1:47132021..47134292-chr1:47182751..47186267,3	MCF-7	breast:
4	chr1:47131887..47139340-chr1:47181784..47186573,11	K562	blood:

Variant related genes	Relation type
EFCAB14	TF binding region
ENSG00000123472	Chromatin interaction
ENSG00000233647	Chromatin interaction
ENSG00000186118	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10158678	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10159351	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025806	0.94[EUR][1000 genomes]
rs1048351	0.94[EUR][1000 genomes]
rs1048380	0.92[EUR][1000 genomes]
rs1075982	0.90[EUR][1000 genomes]
rs10789492	0.82[EUR][1000 genomes]
rs10789493	0.82[EUR][1000 genomes]
rs10890411	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10890415	0.80[EUR][1000 genomes]
rs10890416	0.82[EUR][1000 genomes]
rs11211338	0.92[EUR][1000 genomes]
rs11211341	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11211344	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211349	0.80[EUR][1000 genomes]
rs11211354	0.81[EUR][1000 genomes]
rs1139758	0.91[EUR][1000 genomes]
rs1150064	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1150068	0.88[EUR][1000 genomes]
rs11801316	0.93[EUR][1000 genomes]
rs11801419	0.87[EUR][1000 genomes]
rs11804665	0.91[EUR][1000 genomes]
rs12047537	0.90[EUR][1000 genomes]
rs12078635	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082387	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094663	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1258000	0.81[EUR][1000 genomes]
rs1258004	0.81[ASN][1000 genomes]
rs1258052	0.88[EUR][1000 genomes]
rs1258053	0.88[EUR][1000 genomes]
rs1258054	0.88[EUR][1000 genomes]
rs1258056	0.88[EUR][1000 genomes]
rs1258059	0.88[EUR][1000 genomes]
rs13417	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1440486	0.94[EUR][1000 genomes]
rs1440489	0.85[EUR][1000 genomes]
rs17102352	0.91[EUR][1000 genomes]
rs17102355	0.91[EUR][1000 genomes]
rs17102473	0.97[EUR][1000 genomes]
rs1745377	0.88[EUR][1000 genomes]
rs1933933	0.90[EUR][1000 genomes]
rs1962900	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1971519	0.80[EUR][1000 genomes]
rs2083486	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2119301	0.94[EUR][1000 genomes]
rs2218189	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241862	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289446	0.90[EUR][1000 genomes]
rs2289447	0.87[EUR][1000 genomes]
rs2304745	0.94[EUR][1000 genomes]
rs2405026	0.94[EUR][1000 genomes]
rs2405030	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34932727	0.94[EUR][1000 genomes]
rs3737731	0.94[EUR][1000 genomes]
rs3766211	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3766212	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3766214	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766215	0.94[EUR][1000 genomes]
rs3766217	0.94[EUR][1000 genomes]
rs3766219	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766224	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4272563	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4274009	0.93[EUR][1000 genomes]
rs4301586	0.93[EUR][1000 genomes]
rs4412540	0.80[EUR][1000 genomes]
rs4443838	0.90[EUR][1000 genomes]
rs55914029	0.92[EUR][1000 genomes]
rs56319728	0.80[EUR][1000 genomes]
rs58185502	0.87[EUR][1000 genomes]
rs585257	0.92[EUR][1000 genomes]
rs594118	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs595813	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59881815	0.90[EUR][1000 genomes]
rs60173509	0.90[EUR][1000 genomes]
rs60675294	0.94[EUR][1000 genomes]
rs611468	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs614486	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782563	0.94[EUR][1000 genomes]
rs61782564	0.94[EUR][1000 genomes]
rs61782568	0.94[EUR][1000 genomes]
rs61782590	0.86[EUR][1000 genomes]
rs61784001	0.90[EUR][1000 genomes]
rs61784002	0.90[EUR][1000 genomes]
rs61784003	0.92[EUR][1000 genomes]
rs618554	0.88[EUR][1000 genomes]
rs620431	0.88[EUR][1000 genomes]
rs620913	0.88[EUR][1000 genomes]
rs625507	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs625590	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs637760	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs638845	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6429607	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6429608	0.94[EUR][1000 genomes]
rs6429609	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6429610	0.81[EUR][1000 genomes]
rs647999	0.86[EUR][1000 genomes]
rs6666405	0.88[EUR][1000 genomes]
rs6667885	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6669393	0.91[EUR][1000 genomes]
rs6670495	0.82[EUR][1000 genomes]
rs6671005	0.94[EUR][1000 genomes]
rs6671124	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6688195	0.94[EUR][1000 genomes]
rs6690193	0.80[EUR][1000 genomes]
rs723334	0.89[EUR][1000 genomes]
rs723690	0.81[EUR][1000 genomes]
rs732539	0.92[EUR][1000 genomes]
rs7354865	0.93[EUR][1000 genomes]
rs7412469	0.94[EUR][1000 genomes]
rs744096	0.90[EUR][1000 genomes]
rs7519866	0.94[EUR][1000 genomes]
rs7532601	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534179	0.81[EUR][1000 genomes]
rs7541868	0.92[EUR][1000 genomes]
rs7553243	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8851	0.89[EUR][1000 genomes]
rs946320	0.88[EUR][1000 genomes]

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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11211346	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL
rs11211346	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47184000-47185800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:47184000-47185800	Active TSS	Lung	lung
3	chr1:47185000-47185800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:47185000-47185800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:47185000-47185800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr1:47185000-47185800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:47185000-47185800	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr1:47185000-47185800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr1:47185000-47185800	Flanking Active TSS	Dnd41	blood
10	chr1:47185000-47185800	Flanking Active TSS	GM12878-XiMat	blood
11	chr1:47185000-47185800	Flanking Active TSS	K562	blood
12	chr1:47185200-47185800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:47185200-47185800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:47185200-47185800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:47185200-47185800	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr1:47185200-47185800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr1:47185200-47185800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:47185200-47185800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr1:47185200-47185800	Flanking Active TSS	Thymus	Thymus
20	chr1:47185200-47185800	Flanking Active TSS	Hela-S3	cervix
21	chr1:47185200-47185800	Flanking Active TSS	HepG2	liver
22	chr1:47185200-47189600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:47185200-47189800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:47185400-47185800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:47185400-47185800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:47185400-47185800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:47185400-47185800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr1:47185400-47185800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:47185400-47185800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:47185400-47185800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:47185400-47185800	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:47185400-47185800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr1:47185400-47185800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:47185400-47185800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:47185400-47185800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:47185400-47185800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:47185400-47185800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:47185400-47185800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr1:47185400-47185800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:47185400-47185800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:47185400-47185800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:47185400-47185800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:47185400-47185800	Enhancers	Liver	Liver
44	chr1:47185400-47185800	Enhancers	Fetal Intestine Large	intestine
45	chr1:47185400-47185800	Enhancers	Fetal Intestine Small	intestine
46	chr1:47185400-47185800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:47185400-47185800	Enhancers	Fetal Lung	lung
48	chr1:47185400-47185800	Enhancers	Placenta	Placenta
49	chr1:47185400-47185800	Enhancers	Fetal Stomach	stomach
50	chr1:47185400-47185800	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links