Variant report

Variant	rs2291366
Chromosome Location	chr12:25205801-25205802
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	EP300	chr12:25204678-25206131	GM12878	blood:	n/a	chr12:25205394-25205408 chr12:25205031-25205045
3	POLR2A	chr12:25205254-25205802	GM12891	blood:	n/a	n/a
4	CUX1	chr12:25205475-25205915	K562	blood:	n/a	n/a
5	POLR2A	chr12:25203809-25206210	Raji	blood:	n/a	n/a
6	STAT1	chr12:25205155-25205822	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:25204408-25206309	GM15510	blood:	n/a	n/a
8	EP300	chr12:25204182-25205854	GM12878	blood:	n/a	chr12:25205394-25205408 chr12:25205031-25205045
9	POLR2A	chr12:25204215-25205984	PBDE	blood:	n/a	n/a
10	MYC	chr12:25204152-25206219	NB4	blood:	n/a	chr12:25205483-25205492 chr12:25204668-25204677 chr12:25204670-25204677
11	NFIC	chr12:25204258-25205926	GM12878	blood:	n/a	n/a
12	RUNX3	chr12:25204159-25206177	GM12878	blood:	n/a	chr12:25205125-25205134 chr12:25205125-25205134
13	WRNIP1	chr12:25204169-25206047	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:25204096-25206125	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:25204499-25206137	GM12878	blood:	n/a	n/a
16	CHD2	chr12:25204205-25205838	GM12878	blood:	n/a	n/a
17	BCLAF1	chr12:25204434-25206103	GM12878	blood:	n/a	chr12:25205721-25205730
18	MAX	chr12:25204131-25206227	NB4	blood:	n/a	chr12:25205483-25205492 chr12:25204668-25204677 chr12:25204670-25204677
19	RELA	chr12:25204296-25206061	GM15510	blood:	n/a	n/a
20	STAT5A	chr12:25204679-25205930	GM12878	blood:	n/a	chr12:25205029-25205040
21	POLR2A	chr12:25205156-25206159	GM12892	blood:	n/a	n/a
22	NFATC1	chr12:25204295-25206159	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:25204340-25206102	GM12892	blood:	n/a	n/a
24	CTCF	chr12:25205800-25205950	Caco-2	colon:	n/a	n/a
25	POLR2A	chr12:25205168-25205930	GM12892	blood:	n/a	n/a
26	STAT5A	chr12:25204441-25205997	GM12878	blood:	n/a	chr12:25205029-25205040
27	ELK1	chr12:25204309-25206036	GM12878	blood:	n/a	n/a
28	REST	chr12:25205199-25206226	HL-60	blood:	n/a	chr12:25205721-25205730
29	NFIC	chr12:25204300-25206443	GM12878	blood:	n/a	n/a
30	CUX1	chr12:25204324-25206473	GM12878	blood:	n/a	n/a
31	MXI1	chr12:25203981-25206078	GM12878	blood:	n/a	n/a
32	NFATC1	chr12:25204320-25205926	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:25205113-25206015	HL-60	blood:	n/a	n/a
34	RUNX3	chr12:25204063-25206227	GM12878	blood:	n/a	chr12:25205125-25205134 chr12:25205125-25205134
35	POLR2A	chr12:25204244-25206115	GM19193	blood:	n/a	n/a
36	POLR2A	chr12:25204270-25205983	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:25204088-25206231	GM12891	blood:	n/a	n/a
38	MAZ	chr12:25204102-25206083	GM12878	blood:	n/a	chr12:25205483-25205492 chr12:25204668-25204677 chr12:25204670-25204677
39	YY1	chr12:25204676-25205845	GM12878	blood:	n/a	chr12:25205352-25205362
40	POU2F2	chr12:25205139-25206144	GM12878	blood:	n/a	n/a
41	TAF1	chr12:25204882-25205889	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:25204105-25206480	GM12878	blood:	n/a	n/a
43	SIN3A	chr12:25204479-25205979	GM12878	blood:	n/a	n/a
44	GATA1	chr12:25204247-25206079	PBDE	blood:	n/a	chr12:25204502-25204518 chr12:25204570-25204579 chr12:25204500-25204521
45	EBF1	chr12:25204194-25206068	GM12878	blood:	n/a	n/a
46	MTA3	chr12:25204014-25206071	GM12878	blood:	n/a	n/a
47	SPI1	chr12:25204827-25205869	HL-60	blood:	n/a	chr12:25205437-25205444 chr12:25205608-25205617 chr12:25205393-25205406 chr12:25205793-25205800 chr12:25205395-25205404
48	IRF3	chr12:25205185-25206003	GM12878	blood:	n/a	chr12:25205635-25205645 chr12:25205631-25205645 chr12:25205634-25205647 chr12:25205634-25205646 chr12:25205634-25205647
49	POLR2A	chr12:25204145-25206128	GM12878	blood:	n/a	n/a
50	RFX5	chr12:25204682-25205941	GM12878	blood:	n/a	chr12:25205328-25205341

Variant related genes	Relation type
LRMP	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10505958	0.82[EUR][1000 genomes]
rs11047892	1.00[ASW][hapmap]
rs17329424	1.00[ASW][hapmap]
rs4963601	1.00[ASW][hapmap]
rs4963857	1.00[ASW][hapmap]

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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25204000-25208400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:25204200-25206200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr12:25204200-25208000	Active TSS	Rectal Smooth Muscle	rectum
4	chr12:25204400-25208200	Active TSS	Adipose Nuclei	Adipose
5	chr12:25204400-25209200	Active TSS	Duodenum Mucosa	Duodenum
6	chr12:25204400-25210200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:25204800-25206000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr12:25204800-25206000	Active TSS	Colonic Mucosa	Colon
9	chr12:25204800-25206000	Active TSS	Stomach Smooth Muscle	stomach
10	chr12:25204800-25206200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:25204800-25206200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:25204800-25206200	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr12:25204800-25207200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr12:25204800-25207200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:25204800-25207400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:25204800-25207400	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr12:25204800-25208000	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr12:25204800-25209000	Active TSS	Primary T cells fromperipheralblood	blood
19	chr12:25204800-25209000	Active TSS	Thymus	Thymus
20	chr12:25204800-25209000	Active TSS	GM12878-XiMat	blood
21	chr12:25204800-25209600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:25205000-25206200	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr12:25205000-25206800	Active TSS	Dnd41	blood
24	chr12:25205000-25207600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr12:25205000-25207800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:25205000-25207800	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr12:25205000-25207800	Active TSS	Right Atrium	heart
28	chr12:25205000-25209000	Active TSS	Primary B cells from peripheral blood	blood
29	chr12:25205000-25209000	Active TSS	Fetal Thymus	thymus
30	chr12:25205000-25220000	Weak transcription	Spleen	Spleen
31	chr12:25205200-25206000	Active TSS	Left Ventricle	heart
32	chr12:25205200-25206000	Active TSS	Right Ventricle	heart
33	chr12:25205200-25206200	Flanking Active TSS	Liver	Liver
34	chr12:25205200-25206200	Active TSS	Psoas Muscle	Psoas
35	chr12:25205200-25206200	Active TSS	K562	blood
36	chr12:25205200-25206400	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr12:25205200-25206600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:25205200-25207000	Active TSS	Primary T cells from cord blood	blood
39	chr12:25205200-25207400	Active TSS	Primary B cells from cord blood	blood
40	chr12:25205200-25207600	Active TSS	Brain Hippocampus Middle	brain
41	chr12:25205200-25207600	Active TSS	Fetal Intestine Large	intestine
42	chr12:25205200-25207600	Active TSS	Fetal Intestine Small	intestine
43	chr12:25205400-25206000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:25205400-25206000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:25205400-25206000	Active TSS	Brain Anterior Caudate	brain
46	chr12:25205400-25206000	Active TSS	Brain Cingulate Gyrus	brain
47	chr12:25205400-25206000	Active TSS	Fetal Lung	lung
48	chr12:25205400-25206000	Active TSS	Ovary	ovary
49	chr12:25205400-25206000	Active TSS	Pancreas	Pancrea
50	chr12:25205400-25206000	Active TSS	Osteobl	bone

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