Variant report

Variant	rs17680292
Chromosome Location	chr7:16442361-16442362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16441426..16443801-chr7:16458658..16460792,2	K562	blood:
2	chr7:16438588..16440667-chr7:16440672..16442750,2	K562	blood:
3	chr7:16441360..16443090-chr7:16448119..16450606,2	K562	blood:
4	chr7:16436062..16438376-chr7:16440811..16443657,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10240752	0.81[CEU][hapmap]
rs10257504	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10272029	0.81[CEU][hapmap]
rs10464287	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10950619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11976934	0.93[EUR][1000 genomes]
rs17617900	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56206818	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56223703	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56335840	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60989361	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6461254	0.81[CEU][hapmap]
rs6461255	0.82[EUR][1000 genomes]
rs66743577	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6947550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6949112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6949292	0.81[CEU][hapmap]
rs6955398	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6958802	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6966496	0.80[CEU][hapmap]
rs7457079	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7782939	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9655136	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs9691296	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2759514	chr7:16236162-16527390	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2758105	chr7:16272822-16527390	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv2757215	chr7:16346139-16458474	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv508447	chr7:16360614-16446053	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1031019	chr7:16377519-16458474	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1034151	chr7:16415497-16578081	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17680292	SNX13	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16434400-16459000	Weak transcription	Stomach Mucosa	stomach
2	chr7:16435200-16442800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:16435800-16444400	ZNF genes & repeats	K562	blood
4	chr7:16436200-16443600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr7:16437000-16442600	Weak transcription	Right Ventricle	heart
6	chr7:16439800-16442400	Weak transcription	Brain Anterior Caudate	brain
7	chr7:16439800-16442400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:16439800-16442400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:16439800-16450200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:16440000-16442400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:16440000-16442600	Weak transcription	Brain Angular Gyrus	brain
12	chr7:16440000-16442800	Weak transcription	Liver	Liver
13	chr7:16440000-16442800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:16440000-16449000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:16440200-16442800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:16440200-16443600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:16440200-16452600	Weak transcription	Pancreas	Pancrea
18	chr7:16440400-16442800	Weak transcription	HSMMtube	muscle
19	chr7:16440400-16449000	Weak transcription	HSMM	muscle
20	chr7:16440400-16450000	Weak transcription	Fetal Stomach	stomach
21	chr7:16440400-16450400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:16440400-16452400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:16440400-16452600	Weak transcription	Gastric	stomach
24	chr7:16440400-16459600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:16441200-16445000	Weak transcription	Ovary	ovary
26	chr7:16441600-16443800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:16442000-16442400	Weak transcription	Fetal Lung	lung
28	chr7:16442000-16442600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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