Variant report

Variant	rs2297176
Chromosome Location	chr9:16706012-16706013
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	FOXA2	chr9:16704670-16706096	A549	lung:	n/a	chr9:16705669-16705681

Variant related genes	Relation type
BNC2	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10511624	0.88[ASW][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10511625	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10733313	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10733314	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10733315	0.86[CHB][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10733316	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738445	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs10738446	0.88[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738447	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10738448	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10738449	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10756779	0.90[AFR][1000 genomes]
rs10756781	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10756782	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10756783	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10756784	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756785	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10756786	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10756787	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10810590	0.86[CHB][hapmap]
rs10810591	0.84[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810592	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10810593	0.88[ASW][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10962542	0.88[ASW][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10962546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1337399	0.89[CEU][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1888207	0.88[ASW][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1888208	0.87[CHB][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2297174	0.94[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2383002	0.82[EUR][1000 genomes]
rs2383004	0.89[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3850444	0.83[CEU][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs3850445	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3861709	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3904778	0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs4111334	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4111335	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4360380	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4961732	0.89[CEU][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs4961733	0.83[EUR][1000 genomes]
rs4961734	0.89[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4961735	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4961736	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6651521	0.89[ASN][1000 genomes]
rs7028900	0.89[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv892649	chr9:16677221-16761597	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2297176	SH3GL2	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16691000-16708400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:16702200-16707200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:16704200-16706600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr9:16704200-16706800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:16704800-16706400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:16704800-16706600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr9:16705000-16708600	Weak transcription	Brain Substantia Nigra	brain
8	chr9:16705200-16706200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr9:16705200-16708400	Weak transcription	Aorta	Aorta
10	chr9:16705200-16708600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:16705200-16710600	Weak transcription	Psoas Muscle	Psoas
12	chr9:16705400-16706200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:16705400-16706400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr9:16705400-16706600	Flanking Active TSS	NHLF	lung
15	chr9:16705400-16710600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:16705600-16706400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:16705600-16706400	Enhancers	HSMMtube	muscle
18	chr9:16705600-16706600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:16705600-16706600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:16705600-16706600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr9:16705600-16706600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr9:16705600-16706600	Enhancers	HSMM	muscle
23	chr9:16705600-16706800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr9:16705600-16706800	Enhancers	Colon Smooth Muscle	Colon
25	chr9:16705600-16706800	Enhancers	Fetal Lung	lung
26	chr9:16705600-16706800	Enhancers	Rectal Smooth Muscle	rectum
27	chr9:16705600-16706800	Enhancers	Hela-S3	cervix
28	chr9:16705600-16706800	Enhancers	NH-A	brain
29	chr9:16705600-16706800	Enhancers	NHDF-Ad	bronchial
30	chr9:16705600-16706800	Enhancers	Osteobl	bone
31	chr9:16705600-16707000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr9:16705600-16707000	Enhancers	Stomach Smooth Muscle	stomach
33	chr9:16705600-16707200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr9:16705600-16707400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:16705600-16707600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:16705600-16708200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr9:16705600-16708400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:16705600-16708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:16705600-16708400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr9:16705600-16708400	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:16705600-16708400	Weak transcription	Gastric	stomach
42	chr9:16705600-16708400	Weak transcription	Ovary	ovary
43	chr9:16705600-16708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:16705600-16708600	Weak transcription	Placenta	Placenta
45	chr9:16705600-16708800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:16705600-16708800	Weak transcription	Lung	lung
47	chr9:16705600-16713800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:16705800-16706200	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr9:16705800-16706200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:16705800-16706200	Weak transcription	Fetal Intestine Large	intestine

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