Variant report

Variant	rs7310682
Chromosome Location	chr12:49736702-49736703
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	SP4	chr12:49736047-49736801	H1-hESC	embryonic stem cell:	n/a	chr12:49736755-49736771
2	CTBP2	chr12:49735158-49737394	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr12:49736312-49737428	H1-hESC	embryonic stem cell:	n/a	n/a
4	CCNT2	chr12:49736022-49736785	K562	blood:	n/a	n/a
5	STAT5A	chr12:49736210-49736731	GM12878	blood:	n/a	n/a
6	CTCF	chr12:49735962-49736878	H1-hESC	embryonic stem cell:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
7	RAD21	chr12:49736004-49736793	ECC-1	luminal epithelium:	n/a	chr12:49736374-49736387 chr12:49736375-49736389 chr12:49736375-49736385 chr12:49736371-49736390
8	NR2F2	chr12:49736039-49737343	K562	blood:	n/a	n/a
9	EGR1	chr12:49736077-49736772	H1-hESC	embryonic stem cell:	n/a	chr12:49736754-49736769 chr12:49736761-49736768
10	RAD21	chr12:49736088-49736734	HepG2	liver:	n/a	chr12:49736374-49736387 chr12:49736375-49736389 chr12:49736375-49736385 chr12:49736371-49736390
11	YY1	chr12:49735686-49736751	H1-hESC	embryonic stem cell:	n/a	chr12:49736066-49736077 chr12:49736057-49736071 chr12:49736374-49736388 chr12:49736044-49736055
12	TCF12	chr12:49735929-49737052	A549	lung:	n/a	n/a
13	SETDB1	chr12:49735974-49736724	U2OS	brain:	n/a	n/a
14	RCOR1	chr12:49736043-49736716	K562	blood:	n/a	n/a
15	CTCF	chr12:49735918-49736841	HCT-116	colon:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
16	RAD21	chr12:49735910-49736897	HCT-116	colon:	n/a	chr12:49736789-49736799 chr12:49736374-49736387 chr12:49736375-49736389 chr12:49736375-49736385 chr12:49736371-49736390
17	SMC3	chr12:49735764-49737092	SK-N-SH	brain:	n/a	chr12:49736375-49736385 chr12:49736209-49736219 chr12:49736484-49736498 chr12:49736484-49736494 chr12:49736375-49736389
18	NFIC	chr12:49736096-49737081	ECC-1	luminal epithelium:	n/a	n/a
19	TCF12	chr12:49736309-49736729	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIN3AK20	chr12:49736314-49736818	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr12:49736162-49737386	A549	lung:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
22	SP1	chr12:49736078-49736810	A549	lung:	n/a	chr12:49736147-49736156 chr12:49736145-49736157 chr12:49736145-49736157 chr12:49736146-49736156 chr12:49736744-49736758 chr12:49736146-49736155 chr12:49736142-49736156
23	JUND	chr12:49736437-49736725	H1-hESC	embryonic stem cell:	n/a	chr12:49736615-49736629
24	MTA3	chr12:49736084-49736713	GM12878	blood:	n/a	n/a
25	BHLHE40	chr12:49736173-49737372	K562	blood:	n/a	n/a
26	FOXM1	chr12:49736147-49736711	GM12878	blood:	n/a	n/a
27	CTCF	chr12:49735847-49736887	K562	blood:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
28	TRIM28	chr12:49736183-49736704	K562	blood:	n/a	n/a
29	MAX	chr12:49736021-49736739	K562	blood:	n/a	n/a
30	CTCF	chr12:49736085-49736746	HepG2	liver:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
31	YY1	chr12:49735682-49736746	H1-hESC	embryonic stem cell:	n/a	chr12:49736066-49736077 chr12:49736057-49736071 chr12:49736374-49736388 chr12:49736044-49736055
32	CTCF	chr12:49735652-49736961	SK-N-SH	brain:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736885-49736898 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
33	SIN3AK20	chr12:49736351-49736784	H1-hESC	embryonic stem cell:	n/a	n/a
34	SP1	chr12:49736127-49736916	H1-hESC	embryonic stem cell:	n/a	chr12:49736147-49736156 chr12:49736145-49736157 chr12:49736145-49736157 chr12:49736146-49736156 chr12:49736744-49736758 chr12:49736146-49736155 chr12:49736142-49736156
35	RAD21	chr12:49736062-49737090	SK-N-SH	brain:	n/a	chr12:49736789-49736799 chr12:49736374-49736387 chr12:49736375-49736389 chr12:49736884-49736898 chr12:49736375-49736385 chr12:49736371-49736390
36	PBX3	chr12:49735972-49737011	SK-N-SH	brain:	n/a	n/a
37	CTCF	chr12:49736051-49736710	GM12878	blood:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
38	RAD21	chr12:49736012-49736805	HCT-116	colon:	n/a	chr12:49736789-49736799 chr12:49736374-49736387 chr12:49736375-49736389 chr12:49736375-49736385 chr12:49736371-49736390
39	CREB1	chr12:49736288-49736722	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr12:49736666-49736756	GM19239	blood:	n/a	chr12:49736742-49736755
41	MAX	chr12:49735775-49736813	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr12:49736117-49736715	GM12878	blood:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
43	CTCF	chr12:49735738-49736952	HCT-116	colon:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736885-49736898 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
44	E2F6	chr12:49736239-49737079	A549	lung:	n/a	chr12:49736641-49736648
45	ZBTB7A	chr12:49735808-49737533	ECC-1	luminal epithelium:	n/a	chr12:49736374-49736383 chr12:49736793-49736801
46	RAD21	chr12:49736083-49736717	H1-hESC	embryonic stem cell:	n/a	chr12:49736374-49736387 chr12:49736375-49736389 chr12:49736375-49736385 chr12:49736371-49736390
47	MAX	chr12:49736017-49737563	ECC-1	luminal epithelium:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
48	JUND	chr12:49736359-49736738	H1-hESC	embryonic stem cell:	n/a	chr12:49736615-49736629
49	HDAC2	chr12:49736173-49736865	H1-hESC	embryonic stem cell:	n/a	n/a
50	MYC	chr12:49736092-49736796	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49681784..49683022-chr12:49735866..49736958,14	K562	blood:
2	chr12:49734512..49737434-chr12:49761201..49764804,3	K562	blood:
3	chr12:49656587..49660636-chr12:49733539..49743833,13	K562	blood:
4	chr12:49691373..49692810-chr12:49735826..49736936,11	MCF-7	breast:
5	chr12:49709675..49711213-chr12:49736436..49739309,2	MCF-7	breast:
6	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
7	chr12:49681835..49682776-chr12:49735729..49737096,6	MCF-7	breast:
8	chr12:49725229..49726134-chr12:49735993..49736894,6	MCF-7	breast:
9	chr12:49667825..49672911-chr12:49731373..49736764,7	K562	blood:
10	chr12:49725155..49726080-chr12:49735903..49737150,6	MCF-7	breast:
11	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
12	chr12:49725123..49726098-chr12:49735996..49737262,7	K562	blood:
13	chr12:49685452..49688091-chr12:49734714..49737225,2	MCF-7	breast:
14	chr12:49662709..49665978-chr12:49735321..49738677,4	K562	blood:
15	chr12:49735114..49738057-chr12:49759505..49762701,3	K562	blood:
16	chr12:49690221..49691014-chr12:49736417..49736946,2	K562	blood:
17	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
18	chr12:49665205..49667144-chr12:49734147..49736854,2	MCF-7	breast:
19	chr12:49661766..49665978-chr12:49735321..49738677,5	K562	blood:
20	chr12:49681831..49682839-chr12:49735834..49736883,5	MCF-7	breast:

Variant related genes	Relation type
DNAJC22	TF binding region
ENSG00000258101	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11168981	0.94[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169005	1.00[JPT][hapmap]
rs11169008	1.00[JPT][hapmap]
rs7955245	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7974420	1.00[JPT][hapmap]
rs7980731	1.00[JPT][hapmap]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49734200-49739400	Weak transcription	Hela-S3	cervix
2	chr12:49735000-49737000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:49735400-49737000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr12:49735400-49737000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:49735400-49737200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:49735600-49736800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:49735600-49737000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr12:49735600-49737000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr12:49735600-49737400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:49735800-49736800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr12:49735800-49736800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:49735800-49736800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:49735800-49736800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
14	chr12:49735800-49736800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
15	chr12:49735800-49736800	Active TSS	Brain Angular Gyrus	brain
16	chr12:49735800-49737000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr12:49735800-49737000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
18	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
20	chr12:49735800-49737200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
23	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
24	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
26	chr12:49735800-49737800	Enhancers	Gastric	stomach
27	chr12:49736000-49736800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:49736000-49737000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:49736000-49737000	Active TSS	A549	lung
30	chr12:49736000-49737000	Bivalent/Poised TSS	HSMM	muscle
31	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
32	chr12:49736000-49737200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	NH-A	brain
37	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:49736000-49737400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
41	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
43	chr12:49736000-49737400	Enhancers	Lung	lung
44	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
45	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
46	chr12:49736000-49737600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
47	chr12:49736000-49737800	Enhancers	Pancreas	Pancrea
48	chr12:49736200-49736800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:49736200-49736800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
50	chr12:49736200-49736800	Flanking Active TSS	GM12878-XiMat	blood

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