Variant report

Variant	rs560466550
Chromosome Location	chr12:25205396-25205397
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	RCOR1	chr12:25204462-25205841	GM12878	blood:	n/a	n/a
2	JUND	chr12:25205319-25205716	K562	blood:	n/a	n/a
3	EP300	chr12:25204678-25206131	GM12878	blood:	n/a	chr12:25205394-25205408 chr12:25205031-25205045
4	POLR2A	chr12:25205254-25205802	GM12891	blood:	n/a	n/a
5	BHLHE40	chr12:25204189-25205783	GM12878	blood:	n/a	n/a
6	SPI1	chr12:25205163-25205708	GM12878	blood:	n/a	chr12:25205437-25205444 chr12:25205608-25205617 chr12:25205393-25205406 chr12:25205395-25205404
7	ELF1	chr12:25205108-25205780	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:25203809-25206210	Raji	blood:	n/a	n/a
9	STAT1	chr12:25205155-25205822	GM12878	blood:	n/a	n/a
10	ATF2	chr12:25204452-25205709	GM12878	blood:	n/a	n/a
11	EBF1	chr12:25205192-25205582	GM12878	blood:	n/a	n/a
12	CTCF	chr12:25205380-25205530	GM12873	blood:	n/a	n/a
13	POLR2A	chr12:25204408-25206309	GM15510	blood:	n/a	n/a
14	SPI1	chr12:25205247-25205552	GM12878	blood:	n/a	chr12:25205437-25205444 chr12:25205393-25205406 chr12:25205395-25205404
15	EP300	chr12:25204182-25205854	GM12878	blood:	n/a	chr12:25205394-25205408 chr12:25205031-25205045
16	POLR2A	chr12:25204215-25205984	PBDE	blood:	n/a	n/a
17	MYC	chr12:25204152-25206219	NB4	blood:	n/a	chr12:25205483-25205492 chr12:25204668-25204677 chr12:25204670-25204677
18	NFIC	chr12:25204258-25205926	GM12878	blood:	n/a	n/a
19	RUNX3	chr12:25204159-25206177	GM12878	blood:	n/a	chr12:25205125-25205134 chr12:25205125-25205134
20	WRNIP1	chr12:25204169-25206047	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:25204096-25206125	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:25204499-25206137	GM12878	blood:	n/a	n/a
23	MAFK	chr12:25205340-25205600	HepG2	liver:	n/a	n/a
24	CHD2	chr12:25204205-25205838	GM12878	blood:	n/a	n/a
25	BCLAF1	chr12:25204434-25206103	GM12878	blood:	n/a	chr12:25205721-25205730
26	MAX	chr12:25204131-25206227	NB4	blood:	n/a	chr12:25205483-25205492 chr12:25204668-25204677 chr12:25204670-25204677
27	RELA	chr12:25204296-25206061	GM15510	blood:	n/a	n/a
28	RCOR1	chr12:25205270-25205737	K562	blood:	n/a	n/a
29	MAX	chr12:25204179-25205709	GM12878	blood:	n/a	chr12:25205483-25205492 chr12:25204668-25204677 chr12:25204670-25204677
30	STAT5A	chr12:25204679-25205930	GM12878	blood:	n/a	chr12:25205029-25205040
31	POLR2A	chr12:25205156-25206159	GM12892	blood:	n/a	n/a
32	CTCF	chr12:25205360-25205510	GM12864	blood:	n/a	n/a
33	NRF1	chr12:25205216-25205670	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:25205239-25205790	GM12891	blood:	n/a	n/a
35	NFATC1	chr12:25204295-25206159	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:25204340-25206102	GM12892	blood:	n/a	n/a
37	POLR2A	chr12:25205169-25205793	GM12878	blood:	n/a	n/a
38	YY1	chr12:25205041-25205545	GM12891	blood:	n/a	chr12:25205352-25205362
39	POLR2A	chr12:25205168-25205930	GM12892	blood:	n/a	n/a
40	YY1	chr12:25205092-25205799	GM12892	blood:	n/a	chr12:25205352-25205362
41	SPI1	chr12:25204742-25205724	GM12891	blood:	n/a	chr12:25205437-25205444 chr12:25205608-25205617 chr12:25205393-25205406 chr12:25205395-25205404
42	STAT5A	chr12:25204441-25205997	GM12878	blood:	n/a	chr12:25205029-25205040
43	ELK1	chr12:25204309-25206036	GM12878	blood:	n/a	n/a
44	MAFK	chr12:25205381-25205764	K562	blood:	n/a	n/a
45	REST	chr12:25205199-25206226	HL-60	blood:	n/a	chr12:25205721-25205730
46	TBP	chr12:25205314-25205785	K562	blood:	n/a	n/a
47	NFIC	chr12:25204300-25206443	GM12878	blood:	n/a	n/a
48	POU2F2	chr12:25205317-25205664	GM12878	blood:	n/a	n/a
49	CUX1	chr12:25204324-25206473	GM12878	blood:	n/a	n/a
50	MXI1	chr12:25203981-25206078	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRMP	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription 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 target site	34 gene(s)	inside rSNPs	diseases
3	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
6	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
7	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
9	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases
11	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription 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	14 gene(s)	inside rSNPs	diseases
13	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv52528	chr12:25204785-25213609	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25202800-25205600	Weak transcription	Stomach Mucosa	stomach
2	chr12:25204000-25208400	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr12:25204200-25205400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr12:25204200-25205400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:25204200-25205400	Enhancers	Pancreas	Pancrea
6	chr12:25204200-25205600	Bivalent Enhancer	HepG2	liver
7	chr12:25204200-25206200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr12:25204200-25208000	Active TSS	Rectal Smooth Muscle	rectum
9	chr12:25204400-25205400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr12:25204400-25205800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr12:25204400-25208200	Active TSS	Adipose Nuclei	Adipose
12	chr12:25204400-25209200	Active TSS	Duodenum Mucosa	Duodenum
13	chr12:25204400-25210200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:25204800-25205400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:25204800-25205600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr12:25204800-25205800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr12:25204800-25206000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:25204800-25206000	Active TSS	Colonic Mucosa	Colon
19	chr12:25204800-25206000	Active TSS	Stomach Smooth Muscle	stomach
20	chr12:25204800-25206200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:25204800-25206200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:25204800-25206200	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr12:25204800-25207200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr12:25204800-25207200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:25204800-25207400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:25204800-25207400	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr12:25204800-25208000	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr12:25204800-25209000	Active TSS	Primary T cells fromperipheralblood	blood
29	chr12:25204800-25209000	Active TSS	Thymus	Thymus
30	chr12:25204800-25209000	Active TSS	GM12878-XiMat	blood
31	chr12:25204800-25209600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:25205000-25205800	Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr12:25205000-25206200	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr12:25205000-25206800	Active TSS	Dnd41	blood
35	chr12:25205000-25207600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr12:25205000-25207800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:25205000-25207800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:25205000-25207800	Active TSS	Right Atrium	heart
39	chr12:25205000-25209000	Active TSS	Primary B cells from peripheral blood	blood
40	chr12:25205000-25209000	Active TSS	Fetal Thymus	thymus
41	chr12:25205000-25220000	Weak transcription	Spleen	Spleen
42	chr12:25205200-25205400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr12:25205200-25205400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:25205200-25205400	Flanking Active TSS	Fetal Lung	lung
45	chr12:25205200-25205400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr12:25205200-25205600	Enhancers	Aorta	Aorta
47	chr12:25205200-25205800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr12:25205200-25205800	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr12:25205200-25205800	Active TSS	Fetal Kidney	kidney
50	chr12:25205200-25206000	Active TSS	Left Ventricle	heart

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