Variant report

Variant	rs3800472
Chromosome Location	chr6:34481092-34481093
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	GATA3	chr6:34480716-34481115	SK-N-SH	brain:	n/a	chr6:34480961-34480968 chr6:34480961-34480968 chr6:34480954-34480975 chr6:34480961-34480968 chr6:34480960-34480970
2	GATA3	chr6:34480895-34481107	SH-SY5Y	brain:	n/a	chr6:34480961-34480968 chr6:34480961-34480968 chr6:34480954-34480975 chr6:34480961-34480968 chr6:34480960-34480970
3	GATA2	chr6:34480780-34481138	SH-SY5Y	brain:	n/a	chr6:34480961-34480968 chr6:34480961-34480968 chr6:34480954-34480975 chr6:34480961-34480968 chr6:34480960-34480970

No.	Distal block	Cell Line	Cell type
1	chr6:34467900..34469881-chr6:34479800..34481611,2	K562	blood:
2	chr6:34433077..34435730-chr6:34480474..34482366,2	K562	blood:
3	chr6:34479843..34482340-chr6:34557175..34560153,2	K562	blood:

Variant related genes	Relation type
PACSIN1	TF binding region
ENSG00000124507	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13213617	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2395567	0.92[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3857563	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3997766	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4711394	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713797	0.87[GIH][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap]
rs4713799	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4713800	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4713802	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4713805	0.89[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4713806	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4713807	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7768481	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9357179	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9380441	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9380442	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv462904	chr6:34416388-34493012	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv602903	chr6:34416388-34493012	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv885786	chr6:34426884-34542662	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
9	esv1813536	chr6:34455242-34545123	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv885787	chr6:34458533-34546560	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
11	nsv885788	chr6:34464010-34551912	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
12	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv885789	chr6:34474939-34546560	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34441400-34494000	Weak transcription	Right Atrium	heart
2	chr6:34474800-34481400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:34474800-34481600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:34479000-34485200	Enhancers	Fetal Brain Male	brain
5	chr6:34479600-34482000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr6:34479600-34482000	Enhancers	Brain Angular Gyrus	brain
7	chr6:34479600-34482400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:34479800-34481200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:34479800-34481800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:34480000-34482200	Enhancers	Brain Germinal Matrix	brain
11	chr6:34480400-34482200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:34480400-34482200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:34480400-34482600	Enhancers	K562	blood
14	chr6:34480600-34481400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:34480600-34481400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:34480600-34481600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:34480600-34481600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:34480600-34482200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:34480600-34482200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:34480600-34482200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:34480600-34482200	Enhancers	Fetal Brain Female	brain
22	chr6:34480800-34481600	Weak transcription	Brain Anterior Caudate	brain
23	chr6:34480800-34482200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:34480800-34482400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:34481000-34482000	Enhancers	Brain Cingulate Gyrus	brain

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