Variant report

Variant	rs6946022
Chromosome Location	chr7:7608588-7608589
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	TBP	chr7:7607313-7609708	GM12878	blood:	n/a	n/a
2	MXI1	chr7:7606284-7609622	GM12878	blood:	n/a	n/a
3	BCL11A	chr7:7608586-7609015	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:7606180-7609855	GM12892	blood:	n/a	n/a
5	FOXM1	chr7:7608528-7609113	GM12878	blood:	n/a	n/a
6	EP300	chr7:7608505-7609249	GM12878	blood:	n/a	chr7:7608822-7608836
7	NFATC1	chr7:7608450-7609311	GM12878	blood:	n/a	n/a
8	SIN3A	chr7:7608273-7608972	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr7:7608295-7609722	GM12878	blood:	n/a	n/a
10	MEF2A	chr7:7608537-7609166	GM12878	blood:	n/a	chr7:7608707-7608722
11	CUX1	chr7:7608423-7609094	GM12878	blood:	n/a	n/a
12	ATF2	chr7:7608247-7609672	GM12878	blood:	n/a	n/a
13	RUNX3	chr7:7608559-7609030	GM12878	blood:	n/a	n/a
14	CREB1	chr7:7608511-7609106	GM12878	blood:	n/a	n/a
15	ZNF384	chr7:7608104-7609118	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:7607548-7610838	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:7607549-7609826	GM12892	blood:	n/a	n/a
18	EP300	chr7:7608262-7609101	GM12878	blood:	n/a	chr7:7608822-7608836
19	BCLAF1	chr7:7608244-7609192	GM12878	blood:	n/a	n/a
20	CHD1	chr7:7608203-7609706	GM12878	blood:	n/a	n/a
21	PML	chr7:7608278-7609709	GM12878	blood:	n/a	n/a
22	NFIC	chr7:7608505-7609146	GM12878	blood:	n/a	n/a
23	RUNX3	chr7:7608574-7608965	GM12878	blood:	n/a	n/a
24	SP1	chr7:7608574-7609055	GM12878	blood:	n/a	n/a
25	SPI1	chr7:7608575-7609087	HL-60	blood:	n/a	n/a
26	SP1	chr7:7608575-7609040	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:7606226-7609771	GM12892	blood:	n/a	n/a
28	SPI1	chr7:7608362-7609214	GM12878	blood:	n/a	n/a
29	POLR2A	chr7:7606186-7608743	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr7:7608572-7609721	GM12891	blood:	n/a	n/a
31	ATF2	chr7:7608458-7609151	GM12878	blood:	n/a	n/a
32	POLR2A	chr7:7606063-7609760	GM19099	blood:	n/a	n/a
33	POLR2A	chr7:7608142-7609744	GM12892	blood:	n/a	n/a
34	MEF2A	chr7:7608565-7609149	GM12878	blood:	n/a	chr7:7608707-7608722
35	POLR2A	chr7:7606056-7610648	GM12891	blood:	n/a	n/a
36	NFATC1	chr7:7608506-7610011	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:7606087-7610683	GM12892	blood:	n/a	n/a
38	POLR2A	chr7:7608503-7609682	GM12891	blood:	n/a	n/a
39	RCOR1	chr7:7607566-7609706	GM12878	blood:	n/a	n/a
40	POLR2A	chr7:7607888-7609742	GM12878	blood:	n/a	n/a
41	POLR2A	chr7:7606006-7610933	GM12878	blood:	n/a	n/a
42	SPI1	chr7:7608587-7609090	GM12891	blood:	n/a	n/a
43	POLR2A	chr7:7606174-7610054	GM18505	blood:	n/a	n/a
44	POLR2A	chr7:7606127-7610748	GM12878	blood:	n/a	n/a
45	CREB1	chr7:7608516-7609411	GM12878	blood:	n/a	n/a
46	MTA3	chr7:7606085-7609611	GM12878	blood:	n/a	n/a
47	NFE2	chr7:7608578-7608608	GM12878	blood:	n/a	n/a
48	MAZ	chr7:7608447-7609297	GM12878	blood:	n/a	n/a
49	POLR2A	chr7:7608534-7609665	GM12891	blood:	n/a	n/a
50	NFIC	chr7:7608455-7609120	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7605291..7607922-chr7:7608027..7610593,4	MCF-7	breast:
2	chr7:7588099..7594648-chr7:7604621..7611487,9	MCF-7	breast:
3	chr7:7608142..7610362-chr7:7619716..7621780,2	K562	blood:
4	chr7:7605958..7609334-chr7:7621457..7626452,6	MCF-7	breast:
5	chr7:7220051..7223731-chr7:7605300..7608795,5	K562	blood:

Variant related genes	Relation type
ENSG00000272894	TF binding region
ENSG00000164654	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000272732	Chromatin interaction
ENSG00000106392	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1013002	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1016028	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10229961	0.86[EUR][1000 genomes]
rs10276434	0.86[EUR][1000 genomes]
rs11773679	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11976831	0.95[EUR][1000 genomes]
rs11983756	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12535954	0.91[EUR][1000 genomes]
rs1294600	1.00[AMR][1000 genomes]
rs2051910	0.90[EUR][1000 genomes]
rs2051912	0.90[EUR][1000 genomes]
rs2051913	0.90[EUR][1000 genomes]
rs2051914	0.90[EUR][1000 genomes]
rs2108063	0.86[EUR][1000 genomes]
rs2108064	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2108067	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2190247	0.82[EUR][1000 genomes]
rs2190248	0.95[EUR][1000 genomes]
rs2348265	0.90[EUR][1000 genomes]
rs2348339	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2881888	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2881890	0.86[EUR][1000 genomes]
rs3757532	1.00[CEU][hapmap]
rs4035104	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4380838	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4720741	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4725005	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6463696	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs6463702	1.00[CEU][hapmap]
rs6463705	0.90[EUR][1000 genomes]
rs6946425	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6948157	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6948448	0.87[EUR][1000 genomes]
rs6957976	1.00[CEU][hapmap]
rs6958110	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6962939	0.82[CEU][hapmap]
rs6964397	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6974246	0.90[EUR][1000 genomes]
rs7384200	0.86[EUR][1000 genomes]
rs7783239	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7789187	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7789287	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs7791344	1.00[EUR][1000 genomes]
rs7791808	0.82[CEU][hapmap]
rs7796709	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7801367	0.82[EUR][1000 genomes]
rs7805565	0.90[EUR][1000 genomes]
rs7806046	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7808788	0.95[EUR][1000 genomes]
rs7810367	0.91[EUR][1000 genomes]
rs9640043	0.95[EUR][1000 genomes]
rs9640044	0.90[EUR][1000 genomes]
rs9640045	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs972600	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs974320	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7605800-7608600	Active TSS	NHLF	lung
2	chr7:7606000-7609200	Active TSS	Right Atrium	heart
3	chr7:7606200-7609800	Active TSS	GM12878-XiMat	blood
4	chr7:7607000-7608800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr7:7607000-7609400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr7:7607200-7608600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr7:7607200-7608600	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr7:7607200-7609000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:7607200-7609200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr7:7607200-7609200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:7607200-7609200	Weak transcription	Spleen	Spleen
12	chr7:7607200-7609400	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr7:7607200-7609600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr7:7607200-7609800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr7:7607200-7648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:7607400-7608600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:7607400-7608600	Flanking Active TSS	NHEK	skin
18	chr7:7607400-7608800	Flanking Active TSS	K562	blood
19	chr7:7607400-7609200	Weak transcription	Gastric	stomach
20	chr7:7607400-7609400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:7607400-7609400	Enhancers	Small Intestine	intestine
22	chr7:7607400-7609600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr7:7607400-7610200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:7607400-7612400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
25	chr7:7607400-7646400	Weak transcription	Esophagus	oesophagus
26	chr7:7607400-7648200	Weak transcription	Lung	lung
27	chr7:7607600-7608600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:7607600-7608600	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr7:7607600-7608600	Flanking Active TSS	Fetal Brain Female	brain
30	chr7:7607600-7608600	Flanking Active TSS	Thymus	Thymus
31	chr7:7607600-7608600	Flanking Active TSS	Hela-S3	cervix
32	chr7:7607600-7608800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr7:7607600-7608800	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr7:7607600-7608800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr7:7607600-7608800	Flanking Active TSS	Osteobl	bone
36	chr7:7607600-7609200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr7:7607600-7610600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:7607600-7610600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr7:7607600-7612000	Weak transcription	Ovary	ovary
40	chr7:7607600-7612200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:7607600-7613400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:7607600-7646400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:7607600-7648400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr7:7607800-7608600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr7:7607800-7608600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr7:7607800-7608600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr7:7607800-7608800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:7607800-7608800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr7:7607800-7608800	Enhancers	Fetal Intestine Small	intestine
50	chr7:7607800-7608800	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links