Variant report

Variant	rs4523760
Chromosome Location	chr12:104695009-104695010
allele	C/T
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	POLR2A	chr12:104693383-104695721	Hela-S3	cervix:	n/a	n/a
2	GATA3	chr12:104694639-104695152	MCF-7	breast:	n/a	chr12:104695083-104695092 chr12:104695082-104695092 chr12:104695083-104695092
3	SP1	chr12:104692664-104695225	A549	lung:	n/a	n/a
4	BCL3	chr12:104693440-104696416	A549	lung:	n/a	chr12:104694003-104694012
5	REST	chr12:104694584-104695138	A549	lung:	n/a	n/a
6	MAX	chr12:104694307-104695163	A549	lung:	n/a	n/a
7	CEBPB	chr12:104693872-104695110	A549	lung:	n/a	n/a
8	TCF7L2	chr12:104693590-104695198	PANC-1	pancreas:	n/a	chr12:104694201-104694210 chr12:104694987-104695003 chr12:104694990-104694999
9	GATA3	chr12:104694399-104695126	MCF-7	breast:	n/a	chr12:104695083-104695092 chr12:104695082-104695092 chr12:104695083-104695092
10	POLR2A	chr12:104692660-104695196	HepG2	liver:	n/a	n/a
11	SP1	chr12:104693480-104696248	A549	lung:	n/a	n/a
12	POLR2A	chr12:104693468-104695282	Hela-S3	cervix:	n/a	n/a
13	SIN3AK20	chr12:104693503-104695184	A549	lung:	n/a	n/a
14	BCL3	chr12:104693440-104695125	A549	lung:	n/a	chr12:104694003-104694012
15	POLR2A	chr12:104692579-104696296	HepG2	liver:	n/a	n/a
16	POLR2A	chr12:104692501-104695176	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr12:104684682-104705657	A549	lung:	n/a	n/a
18	EP300	chr12:104693699-104695099	A549	lung:	n/a	chr12:104693998-104694012
19	TCF12	chr12:104692398-104695236	A549	lung:	n/a	chr12:104693776-104693784
20	FOSL2	chr12:104694599-104695216	A549	lung:	n/a	n/a
21	POLR2A	chr12:104692502-104695239	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr12:104693560-104695033	IMR90	lung:	n/a	n/a
23	POLR2A	chr12:104694700-104695063	HCT-116	colon:	n/a	n/a
24	CEBPB	chr12:104693596-104695125	A549	lung:	n/a	n/a
25	POLR2A	chr12:104694665-104695102	K562	blood:	n/a	n/a
26	ATF3	chr12:104694608-104695216	A549	lung:	n/a	n/a
27	POLR2A	chr12:104692649-104695256	Hela-S3	cervix:	n/a	n/a
28	HEY1	chr12:104694963-104695104	HepG2	liver:	n/a	n/a
29	SIN3AK20	chr12:104693555-104695141	A549	lung:	n/a	n/a
30	POLR2A	chr12:104694604-104695172	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr12:104692509-104695262	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104693877..104695820-chr12:104695882..104698208,2	MCF-7	breast:
2	chr12:104681069..104682728-chr12:104694338..104697222,2	MCF-7	breast:
3	chr12:104609017..104611892-chr12:104693747..104695580,2	K562	blood:
4	chr12:104680142..104683904-chr12:104694272..104698636,5	MCF-7	breast:
5	chr12:104683055..104686009-chr12:104694575..104696221,2	MCF-7	breast:

Variant related genes	Relation type
EID3	TF binding region
ENSG00000198431	Chromatin interaction
ENSG00000255150	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10778322	0.84[GIH][hapmap]
rs10861184	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10861188	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111999	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837739	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11838277	1.00[CHB][hapmap]
rs17807362	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs33937214	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35483264	0.87[ASN][1000 genomes]
rs4411337	0.87[GIH][hapmap]
rs4964287	0.84[GIH][hapmap]
rs7134193	1.00[CHB][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315475	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7962942	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974725	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4523760	TCP11L2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104683400-104696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:104683800-104696600	Weak transcription	Brain Anterior Caudate	brain
3	chr12:104683800-104696800	Weak transcription	Fetal Brain Male	brain
4	chr12:104683800-104697000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:104683800-104723800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:104684200-104696600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:104684400-104696600	Weak transcription	Right Atrium	heart
8	chr12:104685800-104696800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:104686000-104696800	Weak transcription	Brain Angular Gyrus	brain
10	chr12:104686200-104696800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:104686200-104700600	Strong transcription	Dnd41	blood
12	chr12:104686400-104697600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:104686800-104696600	Weak transcription	Fetal Intestine Small	intestine
14	chr12:104687200-104696800	Weak transcription	Psoas Muscle	Psoas
15	chr12:104687200-104700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:104687400-104696600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:104687400-104696600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:104687400-104696600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:104687400-104697000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:104687600-104697400	Weak transcription	Gastric	stomach
21	chr12:104688400-104695400	Genic enhancers	HUVEC	blood vessel
22	chr12:104688600-104695600	Enhancers	Stomach Mucosa	stomach
23	chr12:104689400-104696800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:104689400-104696800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:104689600-104696000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:104689600-104696800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:104689600-104696800	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:104689600-104696800	Weak transcription	Fetal Stomach	stomach
29	chr12:104689600-104697400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:104690000-104696000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:104690000-104696600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:104690000-104696600	Weak transcription	Right Ventricle	heart
33	chr12:104690000-104696800	Weak transcription	Fetal Lung	lung
34	chr12:104690000-104696800	Weak transcription	Ovary	ovary
35	chr12:104690000-104696800	Weak transcription	Pancreas	Pancrea
36	chr12:104690200-104695200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:104690200-104696800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:104690200-104696800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:104690200-104696800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:104690200-104696800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:104690200-104696800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:104690200-104697000	Weak transcription	Spleen	Spleen
43	chr12:104690400-104696800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:104690400-104696800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr12:104690400-104697600	Weak transcription	Lung	lung
46	chr12:104690600-104696600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:104690600-104696800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:104690600-104696800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr12:104690600-104697000	Weak transcription	HSMMtube	muscle
50	chr12:104690800-104696600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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