Variant report

Variant	rs35540454
Chromosome Location	chr17:16337583-16337584
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	chr17:16336236-16337593	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:16336081-16341078	K562	blood:	n/a	n/a
3	POLR2A	chr17:16336283-16337589	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:16336233-16337588	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16328263..16331417-chr17:16335355..16337965,3	K562	blood:

Variant related genes	Relation type
TRPV2	TF binding region
FAM211A-AS1	TF binding region
ENSG00000239203	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11078342	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11078343	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11078344	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11653149	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11654069	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11867498	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11869614	0.87[EUR][1000 genomes]
rs11870279	0.85[EUR][1000 genomes]
rs11871017	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11871929	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11871958	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11871963	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12936240	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12938294	0.86[EUR][1000 genomes]
rs12940078	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17552310	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34166276	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34192401	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34419652	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34572942	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34577506	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34779276	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34793697	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34982046	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35034622	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35247166	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35269706	0.83[EUR][1000 genomes]
rs35377488	0.88[EUR][1000 genomes]
rs35474528	0.85[EUR][1000 genomes]
rs35774281	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36117589	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56097826	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7217211	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs941411	0.86[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	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers 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 miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv1065254	chr17:16252880-16389930	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
9	nsv428668	chr17:16265210-16455285	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35540454	C17orf76	cis	frontal cortex	BrainEAC
rs35540454	C17orf45	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16320000-16341400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr17:16323400-16341600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr17:16325200-16341400	Weak transcription	NH-A	brain
4	chr17:16327200-16341400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr17:16327200-16341400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:16327200-16341600	Weak transcription	Left Ventricle	heart
7	chr17:16327200-16341600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr17:16328600-16337600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:16328600-16338000	Strong transcription	Primary T cells from cord blood	blood
10	chr17:16329400-16341400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr17:16329400-16341400	Weak transcription	Fetal Intestine Large	intestine
12	chr17:16329400-16341600	Weak transcription	Liver	Liver
13	chr17:16329600-16341400	Weak transcription	HSMMtube	muscle
14	chr17:16330000-16341400	Weak transcription	NHDF-Ad	bronchial
15	chr17:16330000-16341600	Weak transcription	Colonic Mucosa	Colon
16	chr17:16330400-16341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:16330400-16341600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:16331200-16341600	Weak transcription	HSMM	muscle
19	chr17:16331600-16341600	Weak transcription	Right Ventricle	heart
20	chr17:16331800-16341600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr17:16332000-16338800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:16332000-16341000	Strong transcription	NHLF	lung
23	chr17:16332000-16341200	Weak transcription	Fetal Intestine Small	intestine
24	chr17:16332000-16341400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr17:16332000-16341600	Weak transcription	Colon Smooth Muscle	Colon
26	chr17:16332000-16341600	Weak transcription	Pancreas	Pancrea
27	chr17:16332200-16338000	Weak transcription	HepG2	liver
28	chr17:16332200-16341400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr17:16332600-16338000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:16332600-16341400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr17:16332600-16341400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr17:16332600-16341400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr17:16332600-16341600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:16332600-16341600	Weak transcription	Gastric	stomach
35	chr17:16332600-16341600	Weak transcription	Ovary	ovary
36	chr17:16332600-16341600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr17:16332800-16341400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr17:16332800-16341600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:16333000-16340800	Weak transcription	Dnd41	blood
40	chr17:16333000-16341400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr17:16333000-16341400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr17:16333000-16341400	Weak transcription	K562	blood
43	chr17:16333600-16341400	Weak transcription	Primary B cells from cord blood	blood
44	chr17:16334200-16341400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr17:16334200-16341600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr17:16335600-16339400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:16335600-16341400	Weak transcription	Fetal Thymus	thymus
48	chr17:16335800-16338000	Weak transcription	Placenta	Placenta
49	chr17:16335800-16341400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:16336000-16341400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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