Variant report

Variant	rs930310
Chromosome Location	chr2:11698869-11698870
allele	A/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	SIN3AK20	chr2:11698298-11700553	MCF-7	breast:	n/a	n/a
2	ESR1	chr2:11698772-11699069	T-47D	breast:	n/a	n/a
3	GATA2	chr2:11698283-11699428	SH-SY5Y	brain:	n/a	chr2:11698506-11698513 chr2:11698888-11698898 chr2:11698505-11698515 chr2:11698506-11698515 chr2:11698504-11698516 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698502-11698518
4	GATA3	chr2:11698534-11699190	MCF-7	breast:	n/a	chr2:11698888-11698898 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698889-11698896
5	POLR2A	chr2:11697332-11700490	MCF-7	breast:	n/a	n/a
6	GATA3	chr2:11698322-11699075	T-47D	breast:	n/a	chr2:11698506-11698513 chr2:11698888-11698898 chr2:11698505-11698515 chr2:11698506-11698515 chr2:11698504-11698516 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698502-11698518
7	GATA3	chr2:11698546-11699066	SH-SY5Y	brain:	n/a	chr2:11698888-11698898 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698889-11698896
8	GATA3	chr2:11698358-11699095	T-47D	breast:	n/a	chr2:11698506-11698513 chr2:11698888-11698898 chr2:11698505-11698515 chr2:11698506-11698515 chr2:11698504-11698516 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698502-11698518
9	MXI1	chr2:11696692-11699565	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr2:11698667-11699013	MCF-7	breast:	n/a	chr2:11698888-11698898 chr2:11698889-11698896 chr2:11698889-11698896 chr2:11698889-11698896

No.	Distal block	Cell Line	Cell type
1	chr2:11698164..11701125-chr2:11728905..11731713,2	K562	blood:
2	chr2:11272919..11274870-chr2:11698095..11699910,2	K562	blood:
3	chr2:11260458..11262183-chr2:11697279..11699552,3	MCF-7	breast:

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10495583	0.88[CEU][hapmap]
rs4313952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669751	0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs5020877	0.88[CEU][hapmap]
rs6432210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432214	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432215	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432216	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6432219	0.87[ASN][1000 genomes]
rs6749404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73191479	0.93[ASN][1000 genomes]
rs7565567	0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][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:43 , 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	chr2:11694800-11699200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:11694800-11699600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:11694800-11755200	Weak transcription	Gastric	stomach
7	chr2:11696000-11699800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:11696200-11700400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:11696400-11700200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:11697000-11702200	Weak transcription	Pancreas	Pancrea
11	chr2:11697000-11706800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:11697000-11710800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:11697000-11722600	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:11697000-11723000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:11697000-11723200	Weak transcription	Brain Angular Gyrus	brain
16	chr2:11697400-11699000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:11697600-11699800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:11697600-11699800	Enhancers	Fetal Heart	heart
19	chr2:11697600-11700200	Enhancers	Left Ventricle	heart
20	chr2:11697600-11700400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:11697600-11700600	Transcr. at gene 5' and 3'	Ovary	ovary
22	chr2:11697800-11699000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:11697800-11706800	Weak transcription	Brain Substantia Nigra	brain
24	chr2:11698000-11699000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr2:11698000-11699000	Genic enhancers	HepG2	liver
26	chr2:11698000-11699200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:11698000-11699200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:11698000-11699800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr2:11698200-11699400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:11698200-11699800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr2:11698200-11700000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:11698400-11699000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:11698600-11699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:11698600-11700000	Enhancers	Right Atrium	heart
35	chr2:11698600-11713200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:11698600-11713400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:11698800-11699000	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:11698800-11699200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:11698800-11699600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:11698800-11700400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr2:11698800-11703600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:11698800-11706200	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:11698800-11713400	Weak transcription	H9 Cell Line	embryonic stem cell

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