Variant report

Variant	rs56811883
Chromosome Location	chr2:12003490-12003491
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	chr2:12003400-12003550	GM12868	blood:	n/a	n/a
2	RCOR1	chr2:12003469-12003990	K562	blood:	n/a	n/a
3	ZNF143	chr2:12003438-12004142	GM12878	blood:	n/a	n/a
4	RAD21	chr2:12003334-12004163	GM12878	blood:	n/a	chr2:12003927-12003946
5	CTCF	chr2:12003414-12004844	A549	lung:	n/a	chr2:12003929-12003942 chr2:12003928-12003949 chr2:12003926-12003944 chr2:12003927-12003943
6	YY1	chr2:12003279-12004187	GM12878	blood:	n/a	n/a
7	TBL1XR1	chr2:12003353-12004135	GM12878	blood:	n/a	n/a
8	EP300	chr2:12003384-12003564	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:12003168-12004513	GM12878	blood:	n/a	n/a
10	RUNX3	chr2:12003222-12004239	GM12878	blood:	n/a	n/a
11	BHLHE40	chr2:12003392-12004126	GM12878	blood:	n/a	n/a
12	SMC3	chr2:12003354-12004216	GM12878	blood:	n/a	chr2:12003928-12003942 chr2:12003925-12003932
13	FOXM1	chr2:12003259-12004178	GM12878	blood:	n/a	n/a
14	CTCF	chr2:12003400-12003550	BE2_C	brain:	n/a	n/a
15	CTCF	chr2:12003010-12004877	SK-N-SH	brain:	n/a	chr2:12003929-12003942 chr2:12003928-12003949 chr2:12003357-12003370 chr2:12003926-12003944 chr2:12003927-12003943
16	SMC3	chr2:12003199-12005056	SK-N-SH	brain:	n/a	chr2:12003928-12003942 chr2:12003925-12003932
17	POLR2A	chr2:12001084-12004204	GM12891	blood:	n/a	n/a
18	ATF2	chr2:12003203-12004171	GM12878	blood:	n/a	n/a
19	TCF3	chr2:12003348-12003549	GM12878	blood:	n/a	n/a
20	NFIC	chr2:12003219-12004195	GM12878	blood:	n/a	n/a
21	MXI1	chr2:12003276-12004199	GM12878	blood:	n/a	n/a
22	BCLAF1	chr2:12003255-12004124	GM12878	blood:	n/a	n/a
23	MAZ	chr2:12003296-12004373	GM12878	blood:	n/a	n/a
24	WRNIP1	chr2:12003222-12003980	GM12878	blood:	n/a	n/a
25	RAD21	chr2:12002985-12004840	SK-N-SH	brain:	n/a	chr2:12003927-12003946
26	MAZ	chr2:12003181-12004572	IMR90	lung:	n/a	n/a
27	SP1	chr2:12003260-12004122	GM12878	blood:	n/a	chr2:12003456-12003465 chr2:12003455-12003464
28	ELK1	chr2:12003430-12004135	GM12878	blood:	n/a	n/a
29	MTA3	chr2:12003045-12004442	GM12878	blood:	n/a	n/a
30	MAX	chr2:12003349-12004106	GM12878	blood:	n/a	n/a
31	EP300	chr2:12003433-12004197	GM12878	blood:	n/a	n/a
32	IKZF1	chr2:12003288-12004307	GM12878	blood:	n/a	n/a
33	CTCF	chr2:12003440-12003590	GM12867	blood:	n/a	n/a
34	NFIC	chr2:12003173-12003903	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:12003424..12004525-chr2:12090949..12092302,3	K562	blood:

Variant related genes	Relation type
ENSG00000224184	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16857890	1.00[AMR][1000 genomes]
rs56249556	1.00[AMR][1000 genomes]
rs56709747	1.00[AMR][1000 genomes]
rs57243791	1.00[AMR][1000 genomes]
rs57434799	1.00[AMR][1000 genomes]
rs58449481	1.00[AMR][1000 genomes]
rs59456601	1.00[AMR][1000 genomes]
rs60509666	1.00[AMR][1000 genomes]
rs73915835	1.00[AMR][1000 genomes]
rs73915837	1.00[AMR][1000 genomes]
rs73915838	1.00[AMR][1000 genomes]
rs73915862	1.00[AMR][1000 genomes]
rs73915866	1.00[AMR][1000 genomes]
rs73915868	1.00[AMR][1000 genomes]
rs73915873	1.00[AMR][1000 genomes]
rs73915887	1.00[AMR][1000 genomes]
rs73915888	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
4	nsv833403	chr2:11944552-12125634	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
5	nsv508710	chr2:11982971-12028555	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11994800-12003600	Weak transcription	Gastric	stomach
2	chr2:11999600-12003600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:12000200-12007800	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:12002200-12004600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:12002400-12005200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:12002400-12006800	Enhancers	Primary B cells from cord blood	blood
7	chr2:12002600-12003800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:12002600-12004400	Flanking Active TSS	GM12878-XiMat	blood
9	chr2:12002600-12005000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:12002800-12005000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:12002800-12005000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:12002800-12005400	Enhancers	Spleen	Spleen
13	chr2:12003000-12003600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:12003000-12005000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:12003000-12005000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:12003200-12003600	Enhancers	K562	blood
17	chr2:12003200-12003800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:12003200-12004000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:12003200-12004000	Enhancers	Brain Substantia Nigra	brain
20	chr2:12003200-12004200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:12003200-12004200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr2:12003200-12004400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:12003200-12004400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:12003200-12004400	Enhancers	Fetal Thymus	thymus
25	chr2:12003200-12004600	Enhancers	Fetal Muscle Trunk	muscle
26	chr2:12003200-12004600	Enhancers	Right Ventricle	heart
27	chr2:12003200-12004600	Bivalent Enhancer	HepG2	liver
28	chr2:12003200-12005200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:12003200-12009600	Weak transcription	Right Atrium	heart
30	chr2:12003400-12003600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:12003400-12003600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:12003400-12003600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr2:12003400-12003600	Enhancers	Adipose Nuclei	Adipose
34	chr2:12003400-12003600	Enhancers	Brain Anterior Caudate	brain
35	chr2:12003400-12003600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr2:12003400-12004000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
37	chr2:12003400-12004000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:12003400-12004000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr2:12003400-12004000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr2:12003400-12004000	Enhancers	Fetal Muscle Leg	muscle
41	chr2:12003400-12004200	Enhancers	Primary T cells from cord blood	blood
42	chr2:12003400-12004400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr2:12003400-12004400	Enhancers	Brain Angular Gyrus	brain
44	chr2:12003400-12004400	Enhancers	Brain Cingulate Gyrus	brain
45	chr2:12003400-12004400	Enhancers	Brain Hippocampus Middle	brain
46	chr2:12003400-12004400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:12003400-12004600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:12003400-12004600	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr2:12003400-12004800	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr2:12003400-12004800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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