Variant report

Variant	rs554249272
Chromosome Location	chr7:6629338-6629339
allele	A/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	CTCF	chr7:6629200-6629350	AoAF	blood vessel:	n/a	n/a
2	POLR2A	chr7:6629245-6630402	GM12878	blood:	n/a	n/a
3	NRF1	chr7:6629084-6630389	SK-N-SH	brain:	n/a	chr7:6629523-6629532
4	POLR2A	chr7:6628828-6630384	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr7:6629320-6630101	K562	blood:	n/a	n/a
6	MAX	chr7:6629197-6630487	A549	lung:	n/a	n/a
7	POLR2A	chr7:6629325-6630193	GM19099	blood:	n/a	n/a
8	FOSL2	chr7:6629259-6629817	HepG2	liver:	n/a	n/a
9	HA-E2F1	chr7:6629324-6630258	Hela-S3	cervix:	n/a	chr7:6629523-6629532 chr7:6629776-6629786 chr7:6629734-6629744 chr7:6629720-6629730 chr7:6629673-6629683
10	POLR2A	chr7:6629317-6630667	MCF10A-Er-Src	breast:	n/a	n/a
11	MYBL2	chr7:6629331-6629852	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:6629078-6630303	PANC-1	pancreas:	n/a	n/a
13	CHD2	chr7:6629242-6629948	H1-hESC	embryonic stem cell:	n/a	chr7:6629561-6629571
14	CREB1	chr7:6629329-6630096	A549	lung:	n/a	n/a
15	MAX	chr7:6629266-6630353	A549	lung:	n/a	n/a
16	EP300	chr7:6629256-6630351	SK-N-SH	brain:	n/a	chr7:6629676-6629692 chr7:6629561-6629577 chr7:6629698-6629707 chr7:6629621-6629637 chr7:6629514-6629530 chr7:6629680-6629696
17	FOXP2	chr7:6629325-6630338	PFSK-1	brain:	n/a	n/a
18	NFATC1	chr7:6629333-6629829	GM12878	blood:	n/a	n/a
19	MXI1	chr7:6629195-6630858	IMR90	lung:	n/a	n/a
20	POLR2A	chr7:6629223-6630315	Hela-S3	cervix:	n/a	n/a
21	MAX	chr7:6629146-6630323	ECC-1	luminal epithelium:	n/a	n/a
22	CREB1	chr7:6629248-6630312	HepG2	liver:	n/a	n/a
23	MAX	chr7:6629263-6630522	MCF-7	breast:	n/a	n/a
24	POLR2A	chr7:6629279-6630346	A549	lung:	n/a	n/a
25	JUND	chr7:6629267-6630226	A549	lung:	n/a	n/a
26	HMGN3	chr7:6629312-6630350	K562	blood:	n/a	n/a
27	POLR2A	chr7:6629320-6630357	GM12878	blood:	n/a	n/a
28	POLR2A	chr7:6629259-6630511	H1-neurons	neurons:	n/a	n/a
29	REST	chr7:6629080-6630623	H1-neurons	neurons:	n/a	chr7:6629680-6629690 chr7:6629850-6629863 chr7:6629537-6629550 chr7:6629534-6629547
30	POLR2A	chr7:6629314-6630343	MCF-7	breast:	n/a	n/a
31	POLR2A	chr7:6629274-6630347	HCT-116	colon:	n/a	n/a
32	CTCF	chr7:6629304-6630037	H1-hESC	embryonic stem cell:	n/a	chr7:6629720-6629733 chr7:6629572-6629582 chr7:6629567-6629585 chr7:6629679-6629692 chr7:6629570-6629583 chr7:6629689-6629702 chr7:6629568-6629584 chr7:6629570-6629579 chr7:6629570-6629583
33	EGR1	chr7:6629298-6629774	H1-hESC	embryonic stem cell:	n/a	chr7:6629519-6629533 chr7:6629518-6629531
34	MAZ	chr7:6629321-6630651	IMR90	lung:	n/a	n/a
35	POLR2A	chr7:6629284-6630359	MCF-7	breast:	n/a	n/a
36	POLR2A	chr7:6629299-6630371	Raji	blood:	n/a	n/a
37	POLR2A	chr7:6629251-6630160	K562	blood:	n/a	n/a
38	RCOR1	chr7:6628932-6630633	IMR90	lung:	n/a	n/a
39	HCFC1	chr7:6628947-6630535	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr7:6629320-6630153	GM12878	blood:	n/a	n/a
41	POLR2A	chr7:6629290-6630093	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr7:6629315-6630095	HepG2	liver:	n/a	n/a
43	CTCF	chr7:6629260-6629410	HA-sp	spinal cord:	n/a	n/a
44	CTCF	chr7:6629238-6630060	K562	blood:	n/a	chr7:6629720-6629733 chr7:6629572-6629582 chr7:6629567-6629585 chr7:6629679-6629692 chr7:6629570-6629583 chr7:6629689-6629702 chr7:6629568-6629584 chr7:6629570-6629579 chr7:6629570-6629583
45	POLR2A	chr7:6629283-6630296	GM12892	blood:	n/a	n/a
46	SMC3	chr7:6628384-6630980	SK-N-SH	brain:	n/a	chr7:6629569-6629583 chr7:6629723-6629733 chr7:6629772-6629782 chr7:6629573-6629583 chr7:6629689-6629699
47	CTBP2	chr7:6629266-6630374	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr7:6629313-6630287	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr7:6629224-6630356	SK-N-SH	brain:	n/a	n/a
50	RAD21	chr7:6629302-6629845	SK-N-SH_RA	brain:	n/a	chr7:6629579-6629592 chr7:6629573-6629583 chr7:6629686-6629700 chr7:6629571-6629584 chr7:6629568-6629587 chr7:6629676-6629690

No.	Distal block	Cell Line	Cell type
1	chr7:6523102..6525727-chr7:6628447..6631086,2	MCF-7	breast:
2	chr7:6621445..6626175-chr7:6626576..6631235,7	MCF-7	breast:
3	chr7:6614342..6622557-chr7:6625132..6631922,18	K562	blood:
4	chr7:6615687..6618664-chr7:6627812..6632591,8	MCF-7	breast:
5	chr7:6627960..6631587-chr7:6636185..6643600,9	MCF-7	breast:
6	chr7:6628303..6631132-chr7:6637511..6639950,2	K562	blood:
7	chr7:6627001..6634994-chr7:6673643..6681623,15	MCF-7	breast:
8	chr7:6628726..6630315-chr7:6654459..6656349,2	MCF-7	breast:
9	chr7:6628194..6631157-chr7:6744707..6746398,2	MCF-7	breast:
10	chr7:6628215..6631115-chr7:6675239..6679126,9	MCF-7	breast:
11	chr7:6523333..6525416-chr7:6628158..6630053,2	K562	blood:
12	chr7:6626891..6631454-chr7:6676260..6679154,6	K562	blood:
13	chr7:6628238..6630542-chr7:6653702..6656593,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRID2IP-1	chr7:6628988-6629569	NONHSAT119018

Variant related genes	Relation type
C7orf26	TF binding region
ENSG00000232581	TF binding region
ENSG00000164631	Chromatin interaction
ENSG00000236609	Chromatin interaction
ENSG00000205903	Chromatin interaction
ENSG00000136240	Chromatin interaction
ENSG00000136247	Chromatin interaction
ENSG00000146576	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
4	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
6	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer 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
7	nsv830895	chr7:6514781-6722092	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv887429	chr7:6520676-6659509	Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv887430	chr7:6520676-6668027	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv508444	chr7:6534110-6700527	Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv1025220	chr7:6534278-6736802	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv538717	chr7:6534278-6736802	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv887431	chr7:6535517-6690240	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv515978	chr7:6535517-6698905	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
15	nsv887432	chr7:6535517-6713985	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
16	nsv887433	chr7:6557135-6668027	Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv887434	chr7:6557135-6713985	Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
18	nsv606001	chr7:6563109-6683454	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
19	nsv606002	chr7:6567114-6713985	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
20	nsv887435	chr7:6613604-6713985	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
21	nsv824002	chr7:6618087-6716961	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
22	nsv824003	chr7:6620920-6721409	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
23	nsv887436	chr7:6626922-6721661	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
24	esv1797143	chr7:6628177-6705439	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
25	nsv606003	chr7:6628242-6713985	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
26	esv3381818	chr7:6628877-6630925	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6617600-6629600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:6617600-6629800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:6617600-6630000	Weak transcription	Stomach Mucosa	stomach
4	chr7:6624800-6629600	Weak transcription	Aorta	Aorta
5	chr7:6625000-6629800	Weak transcription	Fetal Kidney	kidney
6	chr7:6625000-6629800	Weak transcription	NHDF-Ad	bronchial
7	chr7:6626800-6629600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:6628000-6629400	Flanking Active TSS	HepG2	liver
9	chr7:6628600-6629400	Weak transcription	Ovary	ovary
10	chr7:6628600-6630400	Active TSS	Rectal Smooth Muscle	rectum
11	chr7:6628800-6629400	Enhancers	Fetal Brain Male	brain
12	chr7:6628800-6629400	Enhancers	Fetal Heart	heart
13	chr7:6628800-6629600	Weak transcription	HSMMtube	muscle
14	chr7:6629000-6629400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:6629000-6629400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr7:6629000-6629400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr7:6629000-6629400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr7:6629000-6629400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:6629000-6629400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:6629000-6629400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:6629000-6629400	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr7:6629000-6629400	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr7:6629000-6629400	Flanking Active TSS	GM12878-XiMat	blood
24	chr7:6629000-6629400	Flanking Active TSS	NHEK	skin
25	chr7:6629000-6629600	Weak transcription	Primary T cells from cord blood	blood
26	chr7:6629000-6629600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr7:6629000-6629600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:6629000-6629600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:6629000-6629600	Enhancers	Fetal Lung	lung
30	chr7:6629000-6629600	Enhancers	Gastric	stomach
31	chr7:6629000-6629600	Enhancers	Lung	lung
32	chr7:6629000-6629600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr7:6629000-6629600	Enhancers	Spleen	Spleen
34	chr7:6629000-6629800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:6629000-6630400	Active TSS	Brain Germinal Matrix	brain
36	chr7:6629000-6630600	Active TSS	Osteobl	bone
37	chr7:6629000-6630800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:6629000-6631000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr7:6629200-6629400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr7:6629200-6629400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:6629200-6629400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:6629200-6629400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr7:6629200-6629400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:6629200-6629400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr7:6629200-6629400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:6629200-6629400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:6629200-6629400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:6629200-6629400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:6629200-6629400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr7:6629200-6629400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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