Variant report

Variant	rs7310815
Chromosome Location	chr12:104613848-104613849
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	MAX	chr12:104613730-104614288	MCF-7	breast:	n/a	n/a
2	EP300	chr12:104613239-104614174	SK-N-SH_RA	brain:	n/a	chr12:104614147-104614157 chr12:104613965-104613974 chr12:104613538-104613547 chr12:104613537-104613546
3	TEAD4	chr12:104613797-104614380	MCF-7	breast:	n/a	n/a
4	FOSL2	chr12:104613064-104614287	A549	lung:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
5	MAX	chr12:104613157-104614174	NB4	blood:	n/a	n/a
6	MAX	chr12:104612509-104614444	A549	lung:	n/a	n/a
7	POLR2A	chr12:104613122-104614212	HCT-116	colon:	n/a	n/a
8	TCF12	chr12:104612894-104614304	ECC-1	luminal epithelium:	n/a	n/a
9	NR3C1	chr12:104613740-104614096	ECC-1	luminal epithelium:	n/a	chr12:104613948-104613957 chr12:104613949-104613958
10	NR3C1	chr12:104613749-104614128	A549	lung:	n/a	chr12:104613948-104613957 chr12:104613949-104613958
11	MAX	chr12:104613714-104614240	SK-N-SH	brain:	n/a	n/a
12	JUN	chr12:104613226-104614170	K562	blood:	n/a	chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
13	FOSL1	chr12:104613720-104614019	K562	blood:	n/a	chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956
14	STAT3	chr12:104613127-104614130	MCF10A-Er-Src	breast:	n/a	chr12:104613538-104613547 chr12:104613537-104613546 chr12:104613970-104613981
15	KAP1	chr12:104612813-104614215	HEK293	kidney:	n/a	n/a
16	PBX3	chr12:104612611-104614205	SK-N-SH	brain:	n/a	n/a
17	MAFK	chr12:104612895-104614214	Hela-S3	cervix:	n/a	n/a
18	STAT3	chr12:104613034-104614212	Hela-S3	cervix:	n/a	chr12:104613538-104613547 chr12:104613537-104613546 chr12:104613970-104613981
19	ZBTB33	chr12:104613002-104614190	A549	lung:	n/a	n/a
20	GATA3	chr12:104613305-104614240	MCF-7	breast:	n/a	chr12:104613939-104613948 chr12:104613938-104613950 chr12:104613476-104613497 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613492
21	REST	chr12:104613695-104614067	PFSK-1	brain:	n/a	n/a
22	MYC	chr12:104613082-104614193	Hela-S3	cervix:	n/a	n/a
23	HDAC2	chr12:104613750-104614073	K562	blood:	n/a	n/a
24	SIX5	chr12:104613090-104614171	A549	lung:	n/a	n/a
25	RXRA	chr12:104613069-104614242	SK-N-SH	brain:	n/a	chr12:104614116-104614125 chr12:104613537-104613546 chr12:104613538-104613547
26	SIN3AK20	chr12:104612693-104614243	A549	lung:	n/a	n/a
27	NFIC	chr12:104612662-104614338	SK-N-SH	brain:	n/a	n/a
28	JUND	chr12:104613001-104614298	A549	lung:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613536-104613547 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
29	JUND	chr12:104613843-104614002	HepG2	liver:	n/a	chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956
30	JUND	chr12:104613186-104614344	MCF-7	breast:	n/a	chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613536-104613547 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
31	SMC3	chr12:104612884-104614139	Hela-S3	cervix:	n/a	n/a
32	MAFF	chr12:104613806-104613989	HepG2	liver:	n/a	n/a
33	FOXA2	chr12:104612941-104614427	A549	lung:	n/a	chr12:104614084-104614096
34	FOS	chr12:104612689-104614196	MCF10A-Er-Src	breast:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613947-104613958 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
35	JUND	chr12:104613015-104614234	Hela-S3	cervix:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613536-104613547 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
36	GATA2	chr12:104613761-104614167	K562	blood:	n/a	chr12:104613939-104613948 chr12:104613938-104613950 chr12:104613938-104613952
37	FOSL2	chr12:104613715-104614129	HepG2	liver:	n/a	chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956
38	JUN	chr12:104613104-104614255	Hela-S3	cervix:	n/a	chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
39	JUND	chr12:104613104-104614154	K562	blood:	n/a	chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613536-104613547 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
40	POLR2A	chr12:104613795-104614071	SK-N-SH	brain:	n/a	n/a
41	CEBPB	chr12:104613154-104614296	MCF-7	breast:	n/a	n/a
42	GABPA	chr12:104613149-104614303	MCF-7	breast:	n/a	n/a
43	TCF7L2	chr12:104613213-104614340	MCF-7	breast:	n/a	n/a
44	SIN3AK20	chr12:104613111-104614468	MCF-7	breast:	n/a	n/a
45	NR3C1	chr12:104613082-104614178	A549	lung:	n/a	chr12:104613948-104613957 chr12:104613949-104613958
46	TAF1	chr12:104613719-104614102	Hela-S3	cervix:	n/a	n/a
47	HMGN3	chr12:104613773-104614104	K562	blood:	n/a	n/a
48	GATA3	chr12:104612552-104614331	SK-N-SH	brain:	n/a	chr12:104613939-104613948 chr12:104613938-104613950 chr12:104613476-104613497 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613492
49	GTF2F1	chr12:104612913-104614172	Hela-S3	cervix:	n/a	n/a
50	MAX	chr12:104613191-104614075	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104613573..104614403-chr3:184080838..184081389,2	Hela-S3	cervix:
2	chr12:104612288..104614036-chr12:104992703..104994366,2	K562	blood:
3	chr12:104611588..104614072-chr12:104619313..104622128,3	K562	blood:
4	chr12:104611665..104617222-chr12:104678192..104683063,15	MCF-7	breast:
5	chr12:104605545..104609502-chr12:104611890..104614832,4	MCF-7	breast:
6	chr12:104612436..104616572-chr12:104617042..104624166,8	MCF-7	breast:
7	chr12:104603545..104605144-chr12:104611962..104614004,2	K562	blood:
8	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
9	chr12:104613560..104615348-chr12:104617225..104620017,2	MCF-7	breast:
10	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000198431	Chromatin interaction
ENSG00000163882	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10778321	0.81[JPT][hapmap]
rs10861185	0.81[JPT][hapmap]
rs10861187	0.81[JPT][hapmap]
rs10861197	0.81[JPT][hapmap]
rs11111913	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11111921	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11111979	0.81[JPT][hapmap]
rs11111980	0.81[JPT][hapmap]
rs11111987	0.81[JPT][hapmap]
rs11536084	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17202060	0.81[JPT][hapmap]
rs2629745	0.83[CEU][hapmap]
rs4595619	0.81[JPT][hapmap]
rs4628754	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964635	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964782	0.81[JPT][hapmap]
rs5018287	0.81[JPT][hapmap]
rs6539125	1.00[CEU][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7294778	0.81[JPT][hapmap]
rs7311546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7487242	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7488680	0.81[JPT][hapmap]
rs7954970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7966740	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7310815	PMCH	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104610200-104614800	Weak transcription	Gastric	stomach
2	chr12:104610800-104614800	Weak transcription	Ovary	ovary
3	chr12:104612000-104614000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:104612000-104615400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:104612200-104614200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:104612200-104615000	Enhancers	HMEC	breast
7	chr12:104612200-104617400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:104612400-104614200	Enhancers	HSMM	muscle
9	chr12:104612400-104616400	Enhancers	Placenta	Placenta
10	chr12:104612600-104615000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:104612800-104614000	Enhancers	Brain Substantia Nigra	brain
12	chr12:104612800-104614000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr12:104612800-104614000	Enhancers	Pancreas	Pancrea
14	chr12:104612800-104614200	Enhancers	Colon Smooth Muscle	Colon
15	chr12:104612800-104614200	Flanking Active TSS	Hela-S3	cervix
16	chr12:104612800-104614200	Enhancers	K562	blood
17	chr12:104612800-104614200	Flanking Active TSS	NH-A	brain
18	chr12:104612800-104614400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:104612800-104614400	Enhancers	Fetal Intestine Large	intestine
20	chr12:104612800-104614800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr12:104612800-104615000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:104612800-104615000	Enhancers	Fetal Stomach	stomach
23	chr12:104613000-104614000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr12:104613000-104614200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:104613000-104614200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:104613000-104614400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:104613000-104614600	Enhancers	HepG2	liver
28	chr12:104613000-104615600	Enhancers	Stomach Mucosa	stomach
29	chr12:104613000-104616000	Enhancers	Duodenum Mucosa	Duodenum
30	chr12:104613200-104614000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:104613200-104614000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:104613200-104614000	Enhancers	Fetal Intestine Small	intestine
33	chr12:104613200-104614000	Enhancers	Rectal Smooth Muscle	rectum
34	chr12:104613200-104614000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:104613200-104614000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:104613200-104614200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:104613200-104614200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:104613200-104614200	Enhancers	Adipose Nuclei	Adipose
39	chr12:104613200-104614400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:104613200-104614400	Active TSS	A549	lung
41	chr12:104613200-104614600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:104613200-104614600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr12:104613400-104614000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:104613400-104614000	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr12:104613400-104614000	Flanking Active TSS	NHEK	skin
46	chr12:104613400-104614000	Flanking Active TSS	Osteobl	bone
47	chr12:104613400-104614200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:104613400-104614200	Enhancers	Primary hematopoietic stem cells	blood
49	chr12:104613400-104614200	Enhancers	Small Intestine	intestine
50	chr12:104613400-104614200	Enhancers	Stomach Smooth Muscle	stomach

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