Variant report

Variant	rs639728
Chromosome Location	chr6:44239922-44239923
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	NR3C1	chr6:44239612-44240144	A549	lung:	n/a	chr6:44239860-44239876 chr6:44239861-44239875 chr6:44239860-44239876 chr6:44239861-44239875 chr6:44239860-44239876 chr6:44239985-44239994
2	FOXA1	chr6:44239688-44239984	A549	lung:	n/a	n/a
3	NR3C1	chr6:44239615-44240080	A549	lung:	n/a	chr6:44239860-44239876 chr6:44239861-44239875 chr6:44239860-44239876 chr6:44239861-44239875 chr6:44239860-44239876 chr6:44239985-44239994
4	NR3C1	chr6:44239645-44239958	A549	lung:	n/a	chr6:44239860-44239876 chr6:44239861-44239875 chr6:44239860-44239876 chr6:44239861-44239875 chr6:44239860-44239876
5	FOXA1	chr6:44239635-44239943	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44231911..44234847-chr6:44237510..44240187,2	MCF-7	breast:
2	chr6:44237771..44241790-chr6:44264717..44266725,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272442	TF binding region
ENSG00000146232	Chromatin interaction
ENSG00000146221	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1283567	0.90[ASN][1000 genomes]
rs167772	0.84[CHD][hapmap]
rs2233437	0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs324137	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs325000	0.81[JPT][hapmap]
rs325001	0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs3799962	0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs483536	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs498512	0.86[JPT][hapmap]
rs513688	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs651297	0.93[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs730775	0.84[CEU][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
12	esv3358306	chr6:44236999-44239947	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	esv3508275	chr6:44237449-44239997	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	esv3508276	chr6:44237449-44239997	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs639728	HSP90AB1	cis	cerebellum	SCAN
rs639728	TCTE1	cis	cerebellum	SCAN
rs639728	CRIP3	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44238000-44240800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:44238800-44241200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:44239000-44240200	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr6:44239000-44240600	Flanking Active TSS	Fetal Brain Female	brain
5	chr6:44239000-44243600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:44239000-44243600	Weak transcription	Right Atrium	heart
7	chr6:44239200-44240200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:44239400-44240000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:44239400-44240000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:44239400-44240800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:44239400-44241200	Active TSS	Brain Cingulate Gyrus	brain
12	chr6:44239400-44243600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:44239600-44240000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:44239600-44240000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
15	chr6:44239600-44240200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr6:44239600-44240400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:44239600-44241000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:44239600-44243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:44239600-44244600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:44239600-44247600	Enhancers	Fetal Brain Male	brain
21	chr6:44239800-44240000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:44239800-44240000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:44239800-44240200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:44239800-44240200	Active TSS	Brain Hippocampus Middle	brain
25	chr6:44239800-44240400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:44239800-44241400	Active TSS	Brain Angular Gyrus	brain
27	chr6:44239800-44242200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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