Variant report

Variant	rs6749404
Chromosome Location	chr2:11697206-11697207
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	GATA3	chr2:11697158-11697574	T-47D	breast:	n/a	n/a
2	EP300	chr2:11697124-11697673	T-47D	breast:	n/a	chr2:11697324-11697334
3	GATA3	chr2:11697179-11697593	T-47D	breast:	n/a	n/a
4	ESR1	chr2:11697144-11697650	T-47D	breast:	n/a	n/a
5	FOXA1	chr2:11697124-11697574	T-47D	breast:	n/a	chr2:11697325-11697337
6	ESR1	chr2:11697170-11697607	T-47D	breast:	n/a	n/a
7	MXI1	chr2:11696692-11699565	SK-N-SH	brain:	n/a	n/a
8	ESR1	chr2:11697189-11697591	T-47D	breast:	n/a	n/a
9	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: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

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];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs5020877	0.90[CEU][hapmap]
rs6432210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];1.00[JPT][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];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432216	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6432219	0.87[ASN][1000 genomes]
rs6718650	0.80[CEU][hapmap]
rs6745409	0.80[CEU][hapmap]
rs73191479	0.93[ASN][1000 genomes]
rs7565567	0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs930310	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]
rs9784028	0.80[CEU][hapmap]

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:33 , 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	chr2:11696400-11700200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:11696800-11697600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:11696800-11697600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:11696800-11697600	Weak transcription	Left Ventricle	heart
22	chr2:11696800-11697800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:11696800-11697800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr2:11696800-11698200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:11697000-11697600	Active TSS	Ovary	ovary
26	chr2:11697000-11697800	Enhancers	Brain Substantia Nigra	brain
27	chr2:11697000-11698600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:11697000-11702200	Weak transcription	Pancreas	Pancrea
29	chr2:11697000-11706800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:11697000-11710800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:11697000-11722600	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:11697000-11723000	Weak transcription	Brain Anterior Caudate	brain
33	chr2:11697000-11723200	Weak transcription	Brain Angular Gyrus	brain

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