Variant report

Variant	rs16857640
Chromosome Location	chr2:11699570-11699571
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr2:11698298-11700553	MCF-7	breast:	n/a	n/a
2	ESR1	chr2:11699255-11699616	T-47D	breast:	n/a	n/a
3	POLR2A	chr2:11697332-11700490	MCF-7	breast:	n/a	n/a
4	GATA3	chr2:11699213-11699715	MCF-7	breast:	n/a	n/a
5	EP300	chr2:11699195-11699736	MCF-7	breast:	n/a	n/a
6	EP300	chr2:11699130-11699680	T-47D	breast:	n/a	n/a
7	GATA3	chr2:11699211-11699651	T-47D	breast:	n/a	n/a
8	TEAD4	chr2:11699298-11699735	MCF-7	breast:	n/a	n/a
9	GATA3	chr2:11699250-11699682	MCF-7	breast:	n/a	n/a
10	FOXA1	chr2:11699153-11699574	T-47D	breast:	n/a	n/a
11	NR2F2	chr2:11699187-11699826	MCF-7	breast:	n/a	chr2:11699551-11699566
12	GATA3	chr2:11699198-11699689	T-47D	breast:	n/a	n/a
13	ZNF217	chr2:11699390-11700103	MCF-7	breast:	n/a	n/a
14	PML	chr2:11699342-11699922	MCF-7	breast:	n/a	n/a
15	ESR1	chr2:11699231-11699573	T-47D	breast:	n/a	n/a
16	EP300	chr2:11699255-11699671	T-47D	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11698164..11701125-chr2:11728905..11731713,2	K562	blood:
2	chr2:11699009..11701296-chr2:218182757..218185396,2	MCF-7	breast:
3	chr2:11679729..11680386-chr2:11699341..11700025,2	MCF-7	breast:
4	chr2:11272919..11274870-chr2:11698095..11699910,2	K562	blood:

No data

Variant related genes	Relation type
RNU2-13P	TF binding region
ENSG00000145063	Chromatin interaction
ENSG00000150873	Chromatin interaction
ENSG00000196208	Chromatin interaction

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[EUR][1000 genomes]
rs16857629	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59563963	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6432218	0.84[CHD][hapmap];0.80[EUR][1000 genomes]
rs6740248	0.84[CHD][hapmap];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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11690000-11711000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:11691400-11699800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:11694800-11699600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:11694800-11755200	Weak transcription	Gastric	stomach
6	chr2:11696000-11699800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:11696200-11700400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:11696400-11700200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:11697000-11702200	Weak transcription	Pancreas	Pancrea
10	chr2:11697000-11706800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:11697000-11710800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:11697000-11722600	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:11697000-11723000	Weak transcription	Brain Anterior Caudate	brain
14	chr2:11697000-11723200	Weak transcription	Brain Angular Gyrus	brain
15	chr2:11697600-11699800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:11697600-11699800	Enhancers	Fetal Heart	heart
17	chr2:11697600-11700200	Enhancers	Left Ventricle	heart
18	chr2:11697600-11700400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:11697600-11700600	Transcr. at gene 5' and 3'	Ovary	ovary
20	chr2:11697800-11706800	Weak transcription	Brain Substantia Nigra	brain
21	chr2:11698000-11699800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:11698200-11699800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:11698200-11700000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:11698600-11699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:11698600-11700000	Enhancers	Right Atrium	heart
26	chr2:11698600-11713200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:11698600-11713400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:11698800-11699600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:11698800-11700400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr2:11698800-11703600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:11698800-11706200	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:11698800-11713400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:11699000-11700400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr2:11699000-11701000	Strong transcription	HepG2	liver
35	chr2:11699000-11714400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:11699200-11699600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:11699200-11699600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:11699400-11699600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:11699400-11699800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:11699400-11700400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:11699400-11706600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:11699400-11706800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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