Variant report

Variant	rs6944061
Chromosome Location	chr7:5013545-5013546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:521)
CpG islands
(count:183)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:521 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr7:5013299-5014399	K562	blood:	n/a	n/a
2	EP300	chr7:5013368-5013923	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr7:5013540-5013690	NHLF	lung:	n/a	n/a
4	YY1	chr7:5013345-5013812	A549	lung:	n/a	n/a
5	MXI1	chr7:5013468-5014570	GM12878	blood:	n/a	n/a
6	FOS	chr7:5013511-5013733	MCF10A-Er-Src	breast:	n/a	n/a
7	TEAD4	chr7:5013351-5013765	K562	blood:	n/a	n/a
8	CTCF	chr7:5013500-5013650	HUVEC	blood vessel:	n/a	n/a
9	CTCF	chr7:5013500-5013650	AG09319	gingival:	n/a	n/a
10	E2F4	chr7:5013532-5014001	MCF10A-Er-Src	breast:	n/a	n/a
11	ZNF384	chr7:5013428-5013725	GM12878	blood:	n/a	n/a
12	CHD2	chr7:5013431-5014382	GM12878	blood:	n/a	chr7:5014128-5014138
13	CTCF	chr7:5013520-5013670	BJ	skin:	n/a	n/a
14	RCOR1	chr7:5013464-5014088	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr7:5013327-5014177	MCF-7	breast:	n/a	n/a
16	POLR2A	chr7:5013427-5013982	HCT-116	colon:	n/a	n/a
17	CTCF	chr7:5013380-5013670	GM12873	blood:	n/a	n/a
18	NRF1	chr7:5013471-5013841	Hela-S3	cervix:	n/a	chr7:5013648-5013659
19	FOSL2	chr7:5013261-5013855	A549	lung:	n/a	n/a
20	PAX5	chr7:5013447-5014271	GM12892	blood:	n/a	chr7:5014247-5014256 chr7:5013831-5013850
21	YY1	chr7:5013366-5013881	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr7:5013500-5013650	HEK293	kidney:	n/a	n/a
23	POLR2A	chr7:5013457-5013846	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr7:5013526-5014072	GM12892	blood:	n/a	n/a
25	POLR2A	chr7:5013347-5014062	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr7:5013517-5013906	U87	brain:	n/a	n/a
27	CTCF	chr7:5013383-5013769	GM10266	blood:	n/a	n/a
28	GATA3	chr7:5013435-5013861	T-47D	breast:	n/a	n/a
29	EGR1	chr7:5013245-5013711	H1-hESC	embryonic stem cell:	n/a	n/a
30	SIN3AK20	chr7:5013318-5014636	SK-N-SH	brain:	n/a	n/a
31	YY1	chr7:5013352-5014010	GM12878	blood:	n/a	n/a
32	ARID3A	chr7:5013472-5013773	HepG2	liver:	n/a	n/a
33	CREB1	chr7:5013385-5014328	A549	lung:	n/a	n/a
34	CTCF	chr7:5013520-5013670	AoAF	blood vessel:	n/a	n/a
35	TBP	chr7:5013390-5013841	HepG2	liver:	n/a	n/a
36	GTF2F1	chr7:5013447-5013796	K562	blood:	n/a	n/a
37	BHLHE40	chr7:5013437-5014320	GM12878	blood:	n/a	chr7:5013793-5013809 chr7:5014073-5014089
38	TAF1	chr7:5013443-5013834	SK-N-SH	brain:	n/a	n/a
39	MAX	chr7:5013479-5014407	A549	lung:	n/a	n/a
40	RCOR1	chr7:5013432-5014064	Hela-S3	cervix:	n/a	n/a
41	TBL1XR1	chr7:5013418-5013789	K562	blood:	n/a	n/a
42	PML	chr7:5013420-5013911	K562	blood:	n/a	n/a
43	GABPA	chr7:5013420-5013839	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr7:5013365-5013813	GM19240	blood:	n/a	n/a
45	HEY1	chr7:5013428-5013979	HepG2	liver:	n/a	chr7:5013928-5013943
46	POLR2A	chr7:5013365-5013899	GM12892	blood:	n/a	n/a
47	CTCF	chr7:5013500-5013650	WERI-Rb-1	eye:	n/a	n/a
48	CTCF	chr7:5013448-5013716	ECC-1	luminal epithelium:	n/a	n/a
49	CTCF	chr7:5013332-5013749	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr7:5013508-5013882	GM12891	blood:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:5013509-5013559	NHBE	bronchial:	n/a
2	chr7:5013536-5013586	AoSMC	blood vessel:	n/a
3	chr7:5013536-5013586	HCM	heart:	n/a
4	chr7:5013536-5013586	CMK	blood:	n/a
5	chr7:5013524-5013574	AG10803	skin:	n/a
6	chr7:5013509-5013559	HNPCEpiC	eye:	n/a
7	chr7:5013524-5013574	HL-60	blood:	n/a
8	chr7:5013509-5013559	SK-N-SH	brain:	n/a
9	chr7:5013536-5013586	Caco-2	colon:	n/a
10	chr7:5013509-5013559	HCPEpiC	choroid plexus:	n/a
11	chr7:5013536-5013586	T-47D	breast:	n/a
12	chr7:5013536-5013586	Hela-S3	cervix:	n/a
13	chr7:5013536-5013586	HMEC	breast:	n/a
14	chr7:5013509-5013559	LNCaP	prostate:	n/a
15	chr7:5013509-5013559	GM06990	blood:	n/a
16	chr7:5013524-5013574	HCT-116	colon:	n/a
17	chr7:5013536-5013586	BE2_C	brain:	n/a
18	chr7:5013524-5013574	RPTEC	kidney:	n/a
19	chr7:5013536-5013586	PANC-1	pancreas:	n/a
20	chr7:5013509-5013559	CMK	blood:	n/a
21	chr7:5013524-5013574	NH-A	brain:	n/a
22	chr7:5013509-5013559	GM12891	blood:	n/a
23	chr7:5013509-5013559	T-47D	breast:	n/a
24	chr7:5013509-5013559	Hela-S3	cervix:	n/a
25	chr7:5013524-5013574	SK-N-SH_RA	brain:	n/a
26	chr7:5013536-5013586	HRPEpiC	eye:	n/a
27	chr7:5013509-5013559	HL-60	blood:	n/a
28	chr7:5013524-5013574	HAEpiC	amniotic membrane:	n/a
29	chr7:5013536-5013586	GM12878	blood:	n/a
30	chr7:5013536-5013586	ECC-1	luminal epithelium:	n/a
31	chr7:5013524-5013574	IMR90	lung:	fetal
32	chr7:5013509-5013559	RPTEC	kidney:	n/a
33	chr7:5013509-5013559	NHDF-neo	bronchial:	n/a
34	chr7:5013509-5013559	HPAEpiC	pulmonary alveolar:	n/a
35	chr7:5013509-5013559	HEEpiC	esophagus:	n/a
36	chr7:5013524-5013574	CMK	blood:	n/a
37	chr7:5013524-5013574	SK-N-SH	brain:	n/a
38	chr7:5013536-5013586	SK-N-SH_RA	brain:	n/a
39	chr7:5013536-5013586	HRE	kidney:	n/a
40	chr7:5013524-5013574	ECC-1	luminal epithelium:	n/a
41	chr7:5013509-5013559	MCF-7	breast:	n/a
42	chr7:5013536-5013586	HAEpiC	amniotic membrane:	n/a
43	chr7:5013536-5013586	NH-A	brain:	n/a
44	chr7:5013536-5013586	GM12891	blood:	n/a
45	chr7:5013509-5013559	HRCEpiC	kidney:	n/a
46	chr7:5013524-5013574	NB4	blood:	n/a
47	chr7:5013509-5013559	HRE	kidney:	n/a
48	chr7:5013509-5013559	HIPEpiC	eye:	n/a
49	chr7:5013509-5013559	SK-N-MC	brain:	n/a
50	chr7:5013509-5013559	AoSMC	blood vessel:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:5012537..5014887-chr7:5022005..5024140,2	K562	blood:
2	chr7:5013311..5013911-chr7:5820908..5821412,3	HCT-116	colon:
3	chr7:5012695..5014428-chr7:5820890..5822170,10	MCF-7	breast:
4	chr7:5012957..5014985-chr7:5085347..5086905,2	MCF-7	breast:
5	chr7:5012217..5014206-chr7:5819722..5821650,2	MCF-7	breast:
6	chr7:5013249..5014674-chr7:5819932..5821408,8	Hela-S3	cervix:
7	chr1:144533720..144534707-chr7:5013377..5013986,2	Hela-S3	cervix:
8	chr7:5012944..5014466-chr7:5819776..5821589,2	MCF-7	breast:
9	chr7:5012983..5015694-chr7:5819277..5821133,2	K562	blood:
10	chr7:4923091..4923826-chr7:5013336..5013934,3	K562	blood:
11	chr7:5012931..5013720-chr7:5820910..5821674,3	MCF-7	breast:
12	chr7:5012284..5014483-chr7:5819277..5821280,2	K562	blood:

No data

Variant related genes	Relation type
RNF216P1	TF binding region
RNF216P1	CpG island
ENSG00000146587	Chromatin interaction
ENSG00000157927	Chromatin interaction
ENSG00000011275	Chromatin interaction
ENSG00000196204	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000272968	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10231607	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10247778	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10274596	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10276341	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10951742	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702058	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2942559	1.00[ASN][1000 genomes]
rs2942565	0.96[EUR][1000 genomes]
rs2965032	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463203	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6463205	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6463207	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67717765	0.83[EUR][1000 genomes]
rs6947228	0.84[EUR][1000 genomes]
rs6949280	0.83[EUR][1000 genomes]
rs6978131	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73046002	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7780482	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7797127	0.84[EUR][1000 genomes]
rs7798542	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7800011	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7802590	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1021170	chr7:4831361-5058033	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv538706	chr7:4831361-5058033	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1025467	chr7:4850447-5021443	ZNF genes & repeats Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1033855	chr7:4862677-5069764	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
13	nsv1019120	chr7:4929653-5138409	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv917078	chr7:4962123-5151633	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
15	nsv525289	chr7:5003373-5083741	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	esv3379760	chr7:5012976-5014924	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5011400-5013600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:5012800-5014800	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr7:5013200-5013600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:5013200-5013600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:5013200-5013600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:5013200-5013600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:5013200-5013600	Flanking Active TSS	Colon Smooth Muscle	Colon
8	chr7:5013200-5013600	Flanking Active TSS	Dnd41	blood
9	chr7:5013200-5013800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:5013200-5014200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:5013200-5014400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr7:5013200-5014400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr7:5013200-5014600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:5013200-5014600	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr7:5013200-5014600	Active TSS	HSMMtube	muscle
16	chr7:5013200-5014800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:5013200-5014800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:5013200-5014800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:5013200-5014800	Active TSS	Colonic Mucosa	Colon
20	chr7:5013200-5014800	Active TSS	Duodenum Mucosa	Duodenum
21	chr7:5013200-5014800	Active TSS	Fetal Stomach	stomach
22	chr7:5013200-5014800	Active TSS	HUVEC	blood vessel
23	chr7:5013200-5014800	Active TSS	NHDF-Ad	bronchial
24	chr7:5013200-5015000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:5013200-5015000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:5013200-5015000	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr7:5013200-5015000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:5013200-5015000	Active TSS	Muscle Satellite Cultured Cells	--
29	chr7:5013200-5015000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:5013200-5015000	Active TSS	Brain Angular Gyrus	brain
31	chr7:5013200-5015000	Active TSS	Brain Anterior Caudate	brain
32	chr7:5013200-5015000	Active TSS	Brain Cingulate Gyrus	brain
33	chr7:5013200-5015000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:5013200-5015000	Active TSS	Fetal Brain Female	brain
35	chr7:5013200-5015000	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr7:5013200-5015000	Active TSS	Stomach Smooth Muscle	stomach
37	chr7:5013200-5015000	Active TSS	A549	lung
38	chr7:5013200-5015000	Active TSS	GM12878-XiMat	blood
39	chr7:5013200-5015000	Active TSS	Osteobl	bone
40	chr7:5013200-5015200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr7:5013200-5015200	Active TSS	Psoas Muscle	Psoas
42	chr7:5013200-5015200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr7:5013200-5015200	Active TSS	Right Ventricle	heart
44	chr7:5013200-5015200	Active TSS	HMEC	breast
45	chr7:5013200-5015200	Active TSS	HSMM	muscle
46	chr7:5013200-5015200	Active TSS	K562	blood
47	chr7:5013200-5015400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:5013200-5015400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:5013200-5015400	Active TSS	Hela-S3	cervix
50	chr7:5013200-5015400	Active TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links