Variant report

Variant	rs798491
Chromosome Location	chr7:2800521-2800522
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	TCF7L2	chr7:2799411-2800583	PANC-1	pancreas:	n/a	chr7:2800034-2800048 chr7:2799527-2799534
2	JUND	chr7:2800217-2800548	K562	blood:	n/a	n/a
3	CTCF	chr7:2799836-2800582	K562	blood:	n/a	chr7:2799932-2799940
4	CTCF	chr7:2800246-2800579	H1-hESC	embryonic stem cell:	n/a	n/a
5	ARID3A	chr7:2800243-2800527	HepG2	liver:	n/a	n/a
6	MAX	chr7:2800297-2800691	NB4	blood:	n/a	n/a
7	RAD21	chr7:2800116-2800620	A549	lung:	n/a	n/a
8	CTCF	chr7:2800247-2800535	GM12878	blood:	n/a	n/a
9	MAX	chr7:2799620-2800540	Hela-S3	cervix:	n/a	chr7:2799768-2799777
10	MAFK	chr7:2800051-2800620	K562	blood:	n/a	n/a
11	MAX	chr7:2799408-2800718	A549	lung:	n/a	chr7:2799609-2799618 chr7:2799768-2799777
12	MAX	chr7:2799646-2800546	Hela-S3	cervix:	n/a	chr7:2799768-2799777
13	MYC	chr7:2800248-2800625	NB4	blood:	n/a	n/a
14	POLR2A	chr7:2800339-2800610	MCF-7	breast:	n/a	n/a
15	CTCF	chr7:2800246-2800566	K562	blood:	n/a	n/a
16	CTCF	chr7:2799091-2801195	SK-N-SH	brain:	n/a	chr7:2799932-2799940 chr7:2800947-2800960 chr7:2800945-2800963 chr7:2799554-2799567
17	CTCF	chr7:2800162-2800594	MCF-7	breast:	n/a	n/a
18	RAD21	chr7:2800212-2800634	MCF-7	breast:	n/a	n/a
19	CTCF	chr7:2799553-2801013	A549	lung:	n/a	chr7:2799932-2799940 chr7:2800947-2800960 chr7:2800945-2800963 chr7:2799554-2799567
20	MAX	chr7:2800306-2800533	K562	blood:	n/a	n/a
21	RAD21	chr7:2800234-2800609	IMR90	lung:	n/a	n/a
22	CTCF	chr7:2800480-2800630	HAc	cerebellar:	n/a	n/a
23	CTCF	chr7:2800278-2800522	SK-N-SH_RA	brain:	n/a	n/a
24	CEBPZ	chr7:2800239-2800524	HepG2	liver:	n/a	n/a
25	MAX	chr7:2799537-2800659	A549	lung:	n/a	chr7:2799609-2799618 chr7:2799768-2799777
26	RAD21	chr7:2800180-2800627	SK-N-SH_RA	brain:	n/a	n/a
27	RAD21	chr7:2800172-2800592	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr7:2800210-2800586	A549	lung:	n/a	n/a
29	MAX	chr7:2800047-2800684	MCF-7	breast:	n/a	n/a
30	CTCF	chr7:2800266-2800530	Gliobla	brain:	n/a	n/a
31	CTCF	chr7:2800334-2800541	MCF-7	breast:	n/a	n/a
32	SP1	chr7:2799744-2800600	A549	lung:	n/a	chr7:2800534-2800548
33	BHLHE40	chr7:2799594-2800567	K562	blood:	n/a	chr7:2799603-2799624
34	MAZ	chr7:2800258-2800525	K562	blood:	n/a	n/a
35	MAX	chr7:2800291-2800660	A549	lung:	n/a	n/a
36	RAD21	chr7:2800245-2800600	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr7:2799879-2800644	K562	blood:	n/a	n/a
38	KAP1	chr7:2800065-2800679	HEK293	kidney:	n/a	n/a
39	CTCF	chr7:2800213-2800612	IMR90	lung:	n/a	n/a
40	CBX3	chr7:2800169-2800649	K562	blood:	n/a	n/a
41	CTCF	chr7:2800440-2800590	WI-38	lung:	n/a	n/a
42	KAP1	chr7:2799927-2800619	U2OS	brain:	n/a	n/a
43	RAD21	chr7:2800175-2800607	HepG2	liver:	n/a	n/a
44	SMC3	chr7:2800234-2800580	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr7:2800203-2800524	H1-hESC	embryonic stem cell:	n/a	n/a
46	TCF12	chr7:2799392-2800672	A549	lung:	n/a	chr7:2800573-2800583 chr7:2799557-2799567 chr7:2799515-2799522
47	HCFC1	chr7:2800354-2800564	K562	blood:	n/a	n/a
48	MAX	chr7:2800192-2800659	K562	blood:	n/a	n/a
49	RAD21	chr7:2799243-2801814	SK-N-SH	brain:	n/a	chr7:2799554-2799564 chr7:2799556-2799570
50	CTCF	chr7:2800257-2800569	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2797400..2800902-chr7:2803018..2805102,3	MCF-7	breast:

Variant related genes	Relation type
GNA12	TF binding region
AMZ1	TF binding region
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1182172	0.83[EUR][1000 genomes]
rs1182174	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1182176	0.85[EUR][1000 genomes]
rs1182177	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182178	0.85[EUR][1000 genomes]
rs1182179	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182181	0.95[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs1182182	0.84[EUR][1000 genomes]
rs1182183	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1182184	0.83[EUR][1000 genomes]
rs1182185	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1182186	0.85[EUR][1000 genomes]
rs1182187	0.87[EUR][1000 genomes]
rs1182188	0.95[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs1182189	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs1182196	0.93[JPT][hapmap]
rs1182198	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1182207	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1182208	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182209	0.85[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1183085	0.85[EUR][1000 genomes]
rs13243214	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1636264	0.91[CEU][hapmap];0.92[JPT][hapmap]
rs1713919	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2107964	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs2158694	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs2260230	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2266922	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2283779	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2527683	0.86[ASN][1000 genomes]
rs2527684	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2527687	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2533878	0.95[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2533879	0.87[EUR][1000 genomes]
rs2533882	0.87[EUR][1000 genomes]
rs2533884	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2644274	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs2644275	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs2644294	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644295	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs2644296	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs2644297	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs2644312	0.95[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs35957220	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6970963	0.83[ASN][1000 genomes]
rs709282	0.94[ASN][1000 genomes]
rs757791	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs7777484	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs7807978	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs798480	0.94[ASN][1000 genomes]
rs798482	0.94[ASN][1000 genomes]
rs798485	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798486	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798487	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798488	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798489	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs798490	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798492	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs798493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798495	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798496	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798498	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798499	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs798500	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798502	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798506	0.90[EUR][1000 genomes]
rs798508	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798511	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798512	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs798513	0.94[ASN][1000 genomes]
rs798514	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798518	0.87[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798526	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798528	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798531	0.94[ASN][1000 genomes]
rs798536	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798540	0.86[ASN][1000 genomes]
rs798544	0.83[ASN][1000 genomes]
rs798545	0.83[ASN][1000 genomes]
rs798546	0.83[ASN][1000 genomes]
rs798547	0.87[ASN][1000 genomes]
rs798548	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs798550	0.87[ASN][1000 genomes]
rs798551	0.87[ASN][1000 genomes]
rs798552	0.87[ASN][1000 genomes]
rs798554	0.82[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs798555	0.91[ASN][1000 genomes]
rs798556	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs798557	0.84[CHB][hapmap];0.91[ASN][1000 genomes]
rs798558	0.87[ASN][1000 genomes]
rs798559	0.88[ASN][1000 genomes]
rs798560	0.88[ASN][1000 genomes]
rs798562	0.90[ASN][1000 genomes]
rs798565	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs960273	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][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	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1032282	chr7:2789555-2820774	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs798491	LOC392620	cis	multi-tissue	Pritchard
rs798491	GNA12	cis	Nerve Tibial	GTEx
rs798491		cis	Lymphoblastoid	GTEx
rs798491	GNA12	cis	multi-tissue	Pritchard
rs798491	GNA12	cis	Artery Tibial	GTEx
rs798491	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2775400-2801200	Weak transcription	Primary T cells from cord blood	blood
2	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr7:2790000-2830400	Weak transcription	Aorta	Aorta
4	chr7:2791200-2803400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:2796400-2800600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr7:2796400-2801000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr7:2796400-2801600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr7:2796400-2803200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr7:2796400-2804000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr7:2796800-2801000	Enhancers	Fetal Intestine Large	intestine
11	chr7:2796800-2802000	Enhancers	Adipose Nuclei	Adipose
12	chr7:2796800-2803600	Weak transcription	Primary B cells from cord blood	blood
13	chr7:2796800-2804400	Enhancers	Fetal Muscle Leg	muscle
14	chr7:2797000-2800800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr7:2797000-2800800	Enhancers	Primary hematopoietic stem cells	blood
16	chr7:2797000-2801000	Enhancers	Brain Germinal Matrix	brain
17	chr7:2797000-2801000	Enhancers	Fetal Thymus	thymus
18	chr7:2797000-2801800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:2797000-2803200	Enhancers	Right Ventricle	heart
20	chr7:2797000-2803800	Enhancers	Brain Cingulate Gyrus	brain
21	chr7:2797000-2805400	Enhancers	Placenta	Placenta
22	chr7:2797200-2801000	Enhancers	Small Intestine	intestine
23	chr7:2797400-2801200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:2797600-2800800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:2797600-2831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr7:2797800-2801000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:2798000-2801200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:2798000-2801400	Enhancers	Psoas Muscle	Psoas
29	chr7:2798000-2803600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr7:2798000-2827400	Weak transcription	Thymus	Thymus
31	chr7:2798200-2800600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr7:2798200-2803200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:2798400-2800600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:2798400-2802000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:2798400-2802200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:2798400-2802200	Enhancers	Osteobl	bone
37	chr7:2798400-2803000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:2798600-2801000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr7:2798600-2801600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:2798600-2802000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:2799000-2800600	Enhancers	Fetal Brain Female	brain
42	chr7:2799000-2801000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:2799000-2801600	Enhancers	Stomach Mucosa	stomach
44	chr7:2799000-2801800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr7:2799000-2803800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr7:2799200-2800600	Enhancers	NH-A	brain
47	chr7:2799200-2800800	Enhancers	GM12878-XiMat	blood
48	chr7:2799200-2801000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:2799200-2801000	Flanking Active TSS	HSMMtube	muscle
50	chr7:2799200-2801200	Enhancers	Fetal Brain Male	brain

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