Variant report

Variant	rs11121482
Chromosome Location	chr1:9777529-9777530
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	CTCF	chr1:9777480-9777630	GM12865	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
2	POLR2A	chr1:9776246-9779771	K562	blood:	n/a	n/a
3	MYC	chr1:9777094-9778017	HepG2	liver:	n/a	chr1:9777426-9777435 chr1:9777777-9777793
4	POLR2A	chr1:9776781-9778603	K562	blood:	n/a	n/a
5	NFIC	chr1:9777269-9778251	HepG2	liver:	n/a	n/a
6	NFYB	chr1:9777418-9778119	K562	blood:	n/a	n/a
7	SRF	chr1:9777436-9777927	K562	blood:	n/a	n/a
8	CTCF	chr1:9777420-9777570	GM06990	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
9	MXI1	chr1:9777373-9777941	GM12878	blood:	n/a	chr1:9777787-9777796
10	PML	chr1:9777271-9778377	K562	blood:	n/a	n/a
11	HDAC2	chr1:9777386-9778042	K562	blood:	n/a	n/a
12	CHD2	chr1:9777292-9778266	GM12878	blood:	n/a	n/a
13	HNF4A	chr1:9777297-9777940	HepG2	liver:	n/a	chr1:9777551-9777563 chr1:9777491-9777506 chr1:9777549-9777564 chr1:9777549-9777564
14	CTCF	chr1:9777354-9777657	GM12878	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
15	CTCF	chr1:9777480-9777630	K562	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
16	FOXA2	chr1:9777400-9777924	HepG2	liver:	n/a	n/a
17	USF1	chr1:9777270-9778115	K562	blood:	n/a	n/a
18	TBP	chr1:9777221-9778392	K562	blood:	n/a	n/a
19	CTCF	chr1:9777400-9777550	GM12872	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
20	ATF3	chr1:9777418-9777965	K562	blood:	n/a	n/a
21	POLR2A	chr1:9775573-9779381	GM12878	blood:	n/a	n/a
22	EP300	chr1:9777322-9778524	K562	blood:	n/a	chr1:9777841-9777850 chr1:9778066-9778082
23	RAD21	chr1:9777394-9777562	K562	blood:	n/a	chr1:9777411-9777421
24	E2F4	chr1:9777031-9778010	K562	blood:	n/a	n/a
25	POLR2A	chr1:9777437-9778228	GM12891	blood:	n/a	n/a
26	TAF1	chr1:9777375-9778039	K562	blood:	n/a	n/a
27	MBD4	chr1:9777433-9778033	HepG2	liver:	n/a	n/a
28	HDAC2	chr1:9777287-9778162	HepG2	liver:	n/a	n/a
29	REST	chr1:9777267-9777662	HepG2	liver:	n/a	chr1:9777300-9777320 chr1:9777413-9777426
30	POLR2A	chr1:9777440-9778188	HL-60	blood:	n/a	n/a
31	EP300	chr1:9777428-9777957	GM12878	blood:	n/a	chr1:9777841-9777850
32	SPI1	chr1:9777292-9778303	GM12878	blood:	n/a	chr1:9777838-9777851 chr1:9777841-9777850 chr1:9777760-9777767
33	CTCF	chr1:9777520-9777670	GM12868	blood:	n/a	n/a
34	CTCF	chr1:9777453-9777628	HepG2	liver:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
35	PML	chr1:9777207-9778058	K562	blood:	n/a	n/a
36	CTCF	chr1:9777480-9777630	GM12871	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
37	CTCF	chr1:9777310-9777673	K562	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
38	GABPA	chr1:9777109-9778189	K562	blood:	n/a	n/a
39	EP300	chr1:9777509-9778066	HepG2	liver:	n/a	chr1:9777841-9777850
40	MAFK	chr1:9777445-9778281	K562	blood:	n/a	n/a
41	POLR2A	chr1:9777423-9778309	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:9777156-9778316	K562	blood:	n/a	n/a
43	CTCF	chr1:9777480-9777630	GM12873	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
44	CTCF	chr1:9777440-9777590	GM12869	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
45	CTCF	chr1:9777420-9777657	GM12891	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
46	POLR2A	chr1:9776174-9780433	K562	blood:	n/a	n/a
47	POLR2A	chr1:9777505-9778055	GM12892	blood:	n/a	n/a
48	CTCF	chr1:9777436-9777613	GM10248	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
49	HNF4A	chr1:9777275-9778005	HepG2	liver:	n/a	chr1:9777551-9777563 chr1:9777491-9777506 chr1:9777549-9777564 chr1:9777549-9777564
50	MBD4	chr1:9777365-9778128	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:9746655..9749475-chr1:9776621..9778385,2	K562	blood:
2	chr1:9746141..9751802-chr1:9775034..9783332,13	K562	blood:
3	chr1:9776353..9779413-chr1:9969324..9972333,3	K562	blood:
4	chr1:9777325..9778983-chr1:9792755..9795426,2	K562	blood:

Variant related genes	Relation type
PIK3CD	TF binding region
ENSG00000171608	Chromatin interaction
ENSG00000171603	Chromatin interaction
ENSG00000231789	Chromatin interaction
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12068953	1.00[MEX][hapmap]
rs12072320	1.00[MEX][hapmap]
rs12084163	1.00[MEX][hapmap]
rs6658971	1.00[MEX][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:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
2	chr1:9751000-9777600	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:9751000-9779800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:9761000-9779000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:9761000-9781600	Weak transcription	HSMMtube	muscle
6	chr1:9761400-9778000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:9763200-9782400	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:9766000-9778800	Weak transcription	NHDF-Ad	bronchial
9	chr1:9766000-9779000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:9766000-9779000	Weak transcription	Osteobl	bone
11	chr1:9766200-9779000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:9768600-9787400	Weak transcription	Left Ventricle	heart
13	chr1:9769200-9783600	Weak transcription	Brain Angular Gyrus	brain
14	chr1:9770200-9778800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:9770800-9782600	Weak transcription	Brain Substantia Nigra	brain
16	chr1:9771400-9777600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:9771600-9782600	Weak transcription	Brain Anterior Caudate	brain
18	chr1:9771800-9778800	Weak transcription	NH-A	brain
19	chr1:9772400-9778800	Weak transcription	HSMM	muscle
20	chr1:9772600-9788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:9773200-9778400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr1:9773400-9778800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:9774000-9778400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:9774400-9777600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:9774600-9777600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:9774600-9783400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:9774800-9782600	Strong transcription	Brain Germinal Matrix	brain
28	chr1:9775000-9777600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:9775200-9779400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
30	chr1:9775400-9777600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:9775400-9782000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:9775600-9779000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:9775600-9779000	Transcr. at gene 5' and 3'	Dnd41	blood
34	chr1:9775600-9783400	Strong transcription	Fetal Brain Female	brain
35	chr1:9775800-9777600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:9776000-9778800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:9776000-9779400	Genic enhancers	Primary monocytes fromperipheralblood	blood
38	chr1:9776000-9779600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:9776200-9777600	Transcr. at gene 5' and 3'	Spleen	Spleen
40	chr1:9776200-9778000	Strong transcription	NHEK	skin
41	chr1:9776200-9778400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:9776200-9778400	Strong transcription	NHLF	lung
43	chr1:9776200-9780000	Genic enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:9776400-9778000	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:9776400-9778800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:9776400-9780000	Enhancers	Placenta	Placenta
47	chr1:9776600-9777800	Transcr. at gene 5' and 3'	Esophagus	oesophagus
48	chr1:9776600-9778200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:9776600-9778400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr1:9776600-9778400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links