Variant report

Variant	rs16857629
Chromosome Location	chr2:11696806-11696807
allele	C/T
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	CEBPB	chr2:11696635-11696871	A549	lung:	n/a	chr2:11696789-11696800
2	REST	chr2:11696571-11696961	MCF-7	breast:	n/a	n/a
3	REST	chr2:11696680-11696843	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr2:11696341-11696806	ProgFib	skin:	n/a	n/a
5	CEBPB	chr2:11696735-11696911	H1-hESC	embryonic stem cell:	n/a	chr2:11696789-11696800
6	SIN3AK20	chr2:11696032-11697143	MCF-7	breast:	n/a	n/a
7	CEBPB	chr2:11696617-11696945	K562	blood:	n/a	chr2:11696789-11696800
8	REST	chr2:11696461-11696899	PFSK-1	brain:	n/a	n/a
9	REST	chr2:11696596-11696909	A549	lung:	n/a	n/a
10	CEBPB	chr2:11696581-11697026	MCF-7	breast:	n/a	chr2:11696789-11696800
11	CEBPB	chr2:11696645-11696943	HepG2	liver:	n/a	chr2:11696789-11696800
12	REST	chr2:11696565-11696920	K562	blood:	n/a	n/a
13	CEBPB	chr2:11696651-11696929	IMR90	lung:	n/a	chr2:11696789-11696800
14	REST	chr2:11696501-11697005	HL-60	blood:	n/a	n/a
15	MXI1	chr2:11696692-11699565	SK-N-SH	brain:	n/a	n/a
16	REST	chr2:11696716-11696806	K562	blood:	n/a	n/a
17	POLR2A	chr2:11695393-11697274	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
RNU2-13P	TF binding region

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13428862	0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16857640	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59563963	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6432218	0.80[EUR][1000 genomes]
rs6740248	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1814335	chr2:11689048-11718858	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11683400-11697800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:11690000-11711000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:11691000-11697600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:11691400-11697600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:11691400-11699800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:11694200-11698400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:11694200-11698400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:11694600-11698200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:11694800-11698000	Strong transcription	HepG2	liver
11	chr2:11694800-11699200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:11694800-11699600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:11694800-11755200	Weak transcription	Gastric	stomach
14	chr2:11696000-11697600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:11696000-11699800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:11696200-11697400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:11696200-11700400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:11696400-11697000	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:11696400-11697000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr2:11696400-11697000	Transcr. at gene 5' and 3'	Ovary	ovary
21	chr2:11696400-11697000	Strong transcription	Pancreas	Pancrea
22	chr2:11696400-11700200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:11696600-11697000	Flanking Active TSS	Brain Angular Gyrus	brain
24	chr2:11696600-11697000	Enhancers	Brain Hippocampus Middle	brain
25	chr2:11696600-11697000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:11696600-11697000	Flanking Active TSS	Brain Substantia Nigra	brain
27	chr2:11696800-11697000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr2:11696800-11697000	Active TSS	Brain Cingulate Gyrus	brain
29	chr2:11696800-11697600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:11696800-11697600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:11696800-11697600	Weak transcription	Left Ventricle	heart
32	chr2:11696800-11697800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:11696800-11697800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr2:11696800-11698200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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