Variant report

Variant	rs16826884
Chromosome Location	chr2:231085172-231085173
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	HCFC1	chr2:231084527-231085338	K562	blood:	n/a	n/a
2	POLR2A	chr2:231084196-231085757	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:231084277-231085227	U87	brain:	n/a	n/a
4	POLR2A	chr2:231084391-231085301	GM12891	blood:	n/a	n/a
5	FOXA1	chr2:231084884-231085180	A549	lung:	n/a	n/a
6	POLR2A	chr2:231084147-231085489	GM12892	blood:	n/a	n/a
7	MAX	chr2:231084197-231085190	A549	lung:	n/a	chr2:231084453-231084464 chr2:231084452-231084462 chr2:231084419-231084429
8	MXI1	chr2:231083977-231085344	IMR90	lung:	n/a	n/a
9	POLR2A	chr2:231084488-231085340	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:231084306-231085274	GM18505	blood:	n/a	n/a
11	MAX	chr2:231084287-231085211	SK-N-SH	brain:	n/a	chr2:231084453-231084464 chr2:231084452-231084462 chr2:231084419-231084429
12	POLR2A	chr2:231084286-231085355	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr2:231084405-231085203	HepG2	liver:	n/a	n/a
14	ZNF263	chr2:231084344-231085308	HEK293-T-REx	kidney:	n/a	chr2:231084909-231084918 chr2:231084912-231084921
15	STAT2	chr2:231084329-231085330	K562	blood:	n/a	chr2:231084741-231084752 chr2:231084739-231084754
16	MYC	chr2:231084301-231085298	NB4	blood:	n/a	chr2:231084453-231084464 chr2:231084452-231084462 chr2:231084419-231084429
17	SIN3AK20	chr2:231084269-231085185	MCF-7	breast:	n/a	n/a
18	HCFC1	chr2:231084224-231085255	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr2:231084313-231085338	GM19193	blood:	n/a	n/a
20	POLR2A	chr2:231084473-231085264	NB4	blood:	n/a	n/a
21	MTA3	chr2:231084167-231085466	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:231085121-231085419	GM12891	blood:	n/a	n/a
23	TCF12	chr2:231084113-231085204	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr2:231084304-231085199	HUVEC	blood vessel:	n/a	n/a
25	MAX	chr2:231084182-231085194	HCT-116	colon:	n/a	chr2:231084453-231084464 chr2:231084452-231084462 chr2:231084419-231084429
26	POLR2A	chr2:231084212-231085428	GM12892	blood:	n/a	n/a
27	ELF1	chr2:231084362-231085218	MCF-7	breast:	n/a	chr2:231084768-231084777 chr2:231085182-231085193 chr2:231084683-231084696
28	RUNX3	chr2:231084262-231085237	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:231084460-231085479	GM12892	blood:	n/a	n/a
30	TBP	chr2:231084620-231085172	HepG2	liver:	n/a	n/a
31	MBD4	chr2:231084491-231085180	HepG2	liver:	n/a	n/a
32	POLR2A	chr2:231084457-231085220	HL-60	blood:	n/a	n/a
33	IRF1	chr2:231084320-231085211	K562	blood:	n/a	chr2:231084740-231084757 chr2:231084740-231084752 chr2:231084733-231084753 chr2:231084738-231084752 chr2:231084740-231084752 chr2:231084737-231084751 chr2:231084741-231084752 chr2:231084735-231084756 chr2:231084741-231084751 chr2:231084739-231084752
34	POLR2A	chr2:231084193-231085445	GM12891	blood:	n/a	n/a
35	YY1	chr2:231085170-231085301	K562	blood:	n/a	chr2:231085249-231085271
36	POLR2A	chr2:231084252-231085190	GM12878	blood:	n/a	n/a
37	PRDM1	chr2:231084095-231085238	Hela-S3	cervix:	n/a	chr2:231085191-231085204 chr2:231084739-231084754 chr2:231084740-231084754 chr2:231084744-231084753
38	POLR2A	chr2:231084309-231085496	GM12878	blood:	n/a	n/a
39	GABPA	chr2:231084335-231085201	MCF-7	breast:	n/a	n/a
40	STAT3	chr2:231084112-231085250	MCF10A-Er-Src	breast:	n/a	chr2:231084727-231084738 chr2:231084741-231084752
41	STAT1	chr2:231084342-231085335	Hela-S3	cervix:	n/a	chr2:231084741-231084752 chr2:231084727-231084738
42	POLR2A	chr2:231084262-231085442	GM19099	blood:	n/a	n/a
43	TBP	chr2:231084414-231085172	Hela-S3	cervix:	n/a	n/a
44	STAT3	chr2:231084247-231085227	MCF10A-Er-Src	breast:	n/a	chr2:231084727-231084738 chr2:231084741-231084752
45	YY1	chr2:231085136-231085392	GM12878	blood:	n/a	chr2:231085249-231085271
46	STAT3	chr2:231083986-231085239	MCF10A-Er-Src	breast:	n/a	chr2:231084727-231084738 chr2:231084741-231084752
47	MYBL2	chr2:231084278-231085172	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:231084288-231085213	SK-N-MC	brain:	n/a	n/a
49	ELF1	chr2:231084304-231085179	SK-N-SH	brain:	n/a	chr2:231084768-231084777 chr2:231084683-231084696
50	ELF1	chr2:231084371-231085182	HCT-116	colon:	n/a	chr2:231084768-231084777 chr2:231084683-231084696

Variant related genes	Relation type
SP110	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16826903	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1896260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57136134	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57654919	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58102716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59268232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59312215	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6729307	0.81[AFR][1000 genomes]
rs6756352	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73104241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73998782	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh 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
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231082400-231085200	Active TSS	Rectal Smooth Muscle	rectum
2	chr2:231082600-231085400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr2:231082600-231085400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr2:231082600-231085600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr2:231083000-231085200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:231083000-231085200	Active TSS	Psoas Muscle	Psoas
7	chr2:231083000-231085200	Active TSS	Right Atrium	heart
8	chr2:231083000-231085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:231083200-231085200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:231083200-231085200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr2:231083200-231085400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr2:231083200-231085400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr2:231083200-231085600	Active TSS	Stomach Smooth Muscle	stomach
14	chr2:231083400-231085200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:231083400-231085200	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr2:231083400-231085200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:231083400-231085200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:231083400-231085200	Active TSS	Colon Smooth Muscle	Colon
19	chr2:231083400-231085600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:231083600-231085200	Active TSS	Thymus	Thymus
21	chr2:231083800-231085200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:231083800-231085200	Active TSS	Ovary	ovary
23	chr2:231084000-231085200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:231084000-231085200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:231084000-231085200	Active TSS	Brain Substantia Nigra	brain
26	chr2:231084000-231085200	Active TSS	Fetal Heart	heart
27	chr2:231084000-231085200	Active TSS	Fetal Muscle Trunk	muscle
28	chr2:231084000-231085200	Active TSS	Fetal Muscle Leg	muscle
29	chr2:231084000-231085200	Active TSS	Right Ventricle	heart
30	chr2:231084000-231085200	Active TSS	NHLF	lung
31	chr2:231084000-231085200	Active TSS	Osteobl	bone
32	chr2:231084000-231085400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:231084000-231085400	Active TSS	Fetal Intestine Small	intestine
34	chr2:231084000-231085400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr2:231084000-231085400	Active TSS	NHDF-Ad	bronchial
36	chr2:231084200-231085200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:231084200-231085200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr2:231084200-231085200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:231084200-231085200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:231084200-231085200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr2:231084200-231085200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:231084200-231085200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:231084200-231085200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:231084200-231085200	Active TSS	Brain Germinal Matrix	brain
45	chr2:231084200-231085200	Active TSS	Esophagus	oesophagus
46	chr2:231084200-231085200	Active TSS	Fetal Intestine Large	intestine
47	chr2:231084200-231085200	Active TSS	Fetal Stomach	stomach
48	chr2:231084200-231085200	Active TSS	Placenta Amnion	Placenta Amnion
49	chr2:231084200-231085200	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr2:231084200-231085200	Active TSS	A549	lung

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