Variant report

Variant	rs17169462
Chromosome Location	chr7:97839140-97839141
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	chr7:97839065-97839479	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:97839105-97839542	K562	blood:	n/a	n/a
3	POLR2A	chr7:97837947-97839595	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
BHLHA15	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10215815	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10235547	0.86[EUR][1000 genomes]
rs10248229	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10254594	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10254691	0.87[EUR][1000 genomes]
rs10258913	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10259449	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10275267	0.82[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10499940	0.86[EUR][1000 genomes]
rs10499944	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12532406	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12539490	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17169406	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2272184	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291748	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3735253	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735256	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72494441	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73404144	0.86[EUR][1000 genomes]
rs73404162	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73406026	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73406034	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7341519	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs754464	0.82[ASW][hapmap]
rs9656054	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer 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	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS 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	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv888761	chr7:97829492-97844578	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv888762	chr7:97829492-97853184	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv888763	chr7:97829492-97866291	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv888764	chr7:97832628-97844578	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS 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	3 gene(s)	inside rSNPs	diseases
17	nsv888765	chr7:97834386-97853184	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv3355961	chr7:97839041-97842189	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17169462	DKFZP434B0335	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97765800-97840800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:97782400-97839800	Weak transcription	Fetal Brain Male	brain
3	chr7:97793400-97841000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:97808600-97839800	Weak transcription	Right Atrium	heart
5	chr7:97812000-97841000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:97816000-97839200	Weak transcription	Psoas Muscle	Psoas
7	chr7:97816600-97839800	Weak transcription	NH-A	brain
8	chr7:97822400-97841000	Weak transcription	K562	blood
9	chr7:97823000-97851000	Weak transcription	HSMMtube	muscle
10	chr7:97823800-97840000	Weak transcription	Small Intestine	intestine
11	chr7:97824400-97839800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:97824600-97839800	Weak transcription	Osteobl	bone
13	chr7:97824600-97840800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:97824800-97839800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:97824800-97839800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:97824800-97840000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:97825200-97851000	Weak transcription	Fetal Lung	lung
18	chr7:97831600-97839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:97832200-97839200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:97832200-97839600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:97832200-97839600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:97832200-97840600	Weak transcription	HMEC	breast
23	chr7:97832400-97839200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:97833600-97840000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:97833800-97841000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:97834600-97841000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr7:97834600-97841000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr7:97835000-97840000	Weak transcription	Primary B cells from cord blood	blood
29	chr7:97835600-97839800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:97835600-97839800	Weak transcription	Colon Smooth Muscle	Colon
31	chr7:97835600-97841000	Weak transcription	HUVEC	blood vessel
32	chr7:97836000-97851000	Weak transcription	NHLF	lung
33	chr7:97836200-97839400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr7:97836400-97839400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:97836400-97839800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr7:97836400-97839800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:97836400-97841000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:97836400-97841000	Weak transcription	GM12878-XiMat	blood
39	chr7:97836600-97839200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr7:97836600-97839400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:97836600-97839400	Weak transcription	Esophagus	oesophagus
42	chr7:97836600-97839400	Weak transcription	Right Ventricle	heart
43	chr7:97836600-97839400	Weak transcription	Spleen	Spleen
44	chr7:97836600-97839600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:97836600-97839600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:97836600-97839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:97836600-97839800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:97836600-97839800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr7:97836600-97839800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:97836600-97839800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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