Variant report

Variant	rs557345497
Chromosome Location	chr3:196360630-196360631
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	POLR2A	chr3:196358486-196362153	NB4	blood:	n/a	n/a
2	CHD2	chr3:196360562-196361500	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:196360370-196361159	GM12892	blood:	n/a	n/a
4	REST	chr3:196360503-196360715	K562	blood:	n/a	n/a
5	REST	chr3:196360407-196360812	PANC-1	pancreas:	n/a	n/a
6	MTA3	chr3:196360242-196361605	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:196358490-196360955	SK-N-MC	brain:	n/a	n/a
8	REST	chr3:196360371-196360755	PFSK-1	brain:	n/a	n/a
9	MAX	chr3:196360563-196361457	NB4	blood:	n/a	chr3:196361330-196361339 chr3:196360809-196360816
10	POLR2A	chr3:196360362-196361052	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:196360577-196360921	MCF-7	breast:	n/a	n/a
12	MAX	chr3:196360463-196361133	K562	blood:	n/a	chr3:196360809-196360816
13	ELF1	chr3:196360425-196361536	GM12878	blood:	n/a	chr3:196360981-196360994
14	POLR2A	chr3:196360499-196360957	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr3:196360374-196361484	GM12878	blood:	n/a	n/a
16	E2F6	chr3:196360541-196360954	K562	blood:	n/a	chr3:196360781-196360792 chr3:196360782-196360794
17	REST	chr3:196360330-196360870	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr3:196360585-196360863	MCF-7	breast:	n/a	n/a
19	POLR2A	chr3:196360307-196361160	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr3:196358547-196361460	GM12892	blood:	n/a	n/a
21	REST	chr3:196360502-196360679	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr3:196360291-196362194	HL-60	blood:	n/a	n/a
23	BHLHE40	chr3:196360622-196360972	K562	blood:	n/a	n/a
24	POLR2A	chr3:196360488-196360724	GM12891	blood:	n/a	n/a
25	MAX	chr3:196360513-196360981	K562	blood:	n/a	chr3:196360809-196360816
26	POLR2A	chr3:196358388-196361043	PBDE	blood:	n/a	n/a
27	POLR2A	chr3:196360275-196361624	HL-60	blood:	n/a	n/a
28	POLR2A	chr3:196360255-196361494	GM12878	blood:	n/a	n/a
29	CHD2	chr3:196360491-196360815	K562	blood:	n/a	n/a
30	POLR2A	chr3:196360426-196361475	GM19193	blood:	n/a	n/a
31	POLR2A	chr3:196360327-196361043	GM12892	blood:	n/a	n/a
32	POLR2A	chr3:196358282-196361457	GM12891	blood:	n/a	n/a
33	POLR2A	chr3:196360386-196361101	GM12891	blood:	n/a	n/a
34	POLR2A	chr3:196360304-196361180	GM12891	blood:	n/a	n/a
35	UBTF	chr3:196360461-196361029	K562	blood:	n/a	n/a
36	REST	chr3:196360474-196360735	PANC-1	pancreas:	n/a	n/a
37	REST	chr3:196360369-196360812	ECC-1	luminal epithelium:	n/a	n/a
38	POU2F2	chr3:196360332-196360793	GM12878	blood:	n/a	n/a
39	SPI1	chr3:196360497-196361734	GM12878	blood:	n/a	chr3:196361290-196361299 chr3:196360987-196361000
40	POLR2A	chr3:196360523-196360694	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr3:196360378-196361481	NB4	blood:	n/a	chr3:196361330-196361339 chr3:196360809-196360816
42	REST	chr3:196360374-196360713	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr3:196360352-196361049	GM12891	blood:	n/a	n/a
44	RELA	chr3:196360388-196361840	GM12891	blood:	n/a	chr3:196361370-196361379 chr3:196361370-196361379
45	POLR2A	chr3:196360371-196361198	K562	blood:	n/a	n/a
46	CBX3	chr3:196360626-196361117	K562	blood:	n/a	n/a
47	POLR2A	chr3:196360565-196360960	GM12878	blood:	n/a	n/a
48	RUNX3	chr3:196360239-196360729	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:196360432-196361050	K562	blood:	n/a	n/a
50	POLR2A	chr3:196360359-196361147	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196359722..196361449-chr3:196369958..196371504,2	MCF-7	breast:
2	chr14:30396875..30399384-chr3:196359205..196361217,2	MCF-7	breast:
3	chr3:196293733..196296360-chr3:196359092..196361282,2	MCF-7	breast:
4	chr3:196312738..196315414-chr3:196359776..196362202,2	K562	blood:
5	chr3:196360616..196362488-chr3:196400415..196403548,3	K562	blood:

Variant related genes	Relation type
LINC01063	TF binding region
ENSG00000185798	Chromatin interaction
ENSG00000184304	Chromatin interaction
ENSG00000174013	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv1003135	chr3:196348721-196738953	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
10	esv3396603	chr3:196360505-196362903	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196359200-196360800	Active TSS	Rectal Smooth Muscle	rectum
2	chr3:196359400-196360800	Enhancers	Fetal Brain Male	brain
3	chr3:196359600-196362200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:196359800-196361000	Flanking Active TSS	Primary B cells from peripheral blood	blood
5	chr3:196359800-196361200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr3:196359800-196361200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:196359800-196361400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr3:196359800-196361400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr3:196359800-196361400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:196359800-196362200	Flanking Active TSS	Fetal Thymus	thymus
11	chr3:196359800-196362200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr3:196360000-196360800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:196360000-196361000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr3:196360000-196361000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:196360000-196361000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:196360000-196361000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr3:196360000-196361000	Enhancers	Fetal Lung	lung
18	chr3:196360000-196361000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:196360000-196361400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:196360000-196362000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:196360000-196363000	Weak transcription	NHDF-Ad	bronchial
22	chr3:196360000-196366200	Weak transcription	Esophagus	oesophagus
23	chr3:196360200-196360800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:196360200-196360800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr3:196360200-196360800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:196360200-196360800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:196360200-196360800	Enhancers	Brain Anterior Caudate	brain
28	chr3:196360200-196360800	Weak transcription	Colonic Mucosa	Colon
29	chr3:196360200-196360800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr3:196360200-196360800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:196360200-196360800	Enhancers	Fetal Heart	heart
32	chr3:196360200-196360800	Enhancers	Fetal Intestine Small	intestine
33	chr3:196360200-196360800	Enhancers	Fetal Stomach	stomach
34	chr3:196360200-196360800	Enhancers	Pancreas	Pancrea
35	chr3:196360200-196360800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:196360200-196360800	Enhancers	Small Intestine	intestine
37	chr3:196360200-196361000	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr3:196360200-196361000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:196360200-196361000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:196360200-196361000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr3:196360200-196361000	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:196360200-196361000	Enhancers	Fetal Intestine Large	intestine
43	chr3:196360200-196361000	Enhancers	Lung	lung
44	chr3:196360200-196361200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:196360200-196361200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:196360200-196361200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:196360200-196361400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:196360200-196361400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr3:196360200-196361400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:196360200-196361400	Enhancers	HepG2	liver

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