Variant report

Variant	rs2293509
Chromosome Location	chr7:70231070-70231071
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	POLR2A	chr7:70226672-70231239	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:70225557-70231872	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:70230818-70231451	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr7:70230884-70231102	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:70229330-70231957	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr7:70226736-70231526	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
AUTS2	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10950212	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11766719	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11768020	0.90[ASN][1000 genomes]
rs12671262	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12673908	0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs13227667	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1544009	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1569079	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35363074	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3750170	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460555	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460556	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6955943	0.96[ASN][1000 genomes]
rs6959459	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6960426	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73181096	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73445005	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7782110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532783	chr7:69939570-70245396	Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv3341834	chr7:69968031-70288098	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1025164	chr7:70061655-70469358	Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538931	chr7:70061655-70469358	Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1017876	chr7:70073764-70434599	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1022747	chr7:70169254-70301285	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv429771	chr7:70188375-70294296	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv831022	chr7:70189351-70238179	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1028853	chr7:70211620-70523331	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv533212	chr7:70220687-70511129	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2293509	BAZ1B	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70214800-70250000	Weak transcription	Psoas Muscle	Psoas
2	chr7:70218200-70231200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr7:70218600-70241600	Weak transcription	Fetal Heart	heart
4	chr7:70222000-70258000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:70223200-70238000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:70223400-70237400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:70224600-70231200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:70225400-70232800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:70226400-70254800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:70227400-70233400	Strong transcription	Fetal Stomach	stomach
11	chr7:70227400-70237400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:70227400-70253000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:70227600-70232000	Strong transcription	Fetal Intestine Small	intestine
14	chr7:70227600-70233400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:70227600-70234600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:70227600-70236600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:70227600-70237400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:70227600-70241400	Strong transcription	Dnd41	blood
19	chr7:70227800-70232400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:70228000-70231800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:70228000-70249400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:70228200-70236200	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:70228400-70231400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:70228400-70236400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr7:70228400-70250000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:70228400-70257400	Weak transcription	Right Atrium	heart
27	chr7:70228600-70238400	Strong transcription	Primary T cells from cord blood	blood
28	chr7:70228600-70238600	Weak transcription	Brain Angular Gyrus	brain
29	chr7:70228800-70238000	Weak transcription	Brain Substantia Nigra	brain
30	chr7:70228800-70241600	Weak transcription	NHDF-Ad	bronchial
31	chr7:70229000-70232200	Strong transcription	Esophagus	oesophagus
32	chr7:70229000-70234600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:70229000-70239200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr7:70229200-70232200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:70229200-70234800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:70229200-70236600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:70229400-70232200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr7:70229400-70240200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr7:70229400-70259600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr7:70229400-70259600	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr7:70229600-70232000	Strong transcription	Fetal Brain Female	brain
42	chr7:70229600-70235200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:70229600-70236800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr7:70229600-70240200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr7:70229600-70241600	Strong transcription	Fetal Muscle Leg	muscle
46	chr7:70229600-70242200	Weak transcription	Small Intestine	intestine
47	chr7:70229800-70232000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:70229800-70232000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:70229800-70232000	Strong transcription	Lung	lung
50	chr7:70229800-70232000	Strong transcription	Thymus	Thymus

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