Variant report

Variant	rs197926
Chromosome Location	chr17:45012087-45012088
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	POLR2A	chr17:45011949-45014116	K562	blood:	n/a	n/a
2	POLR2A	chr17:45011945-45012292	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr17:45011988-45012317	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45006450..45009372-chr17:45011521..45013719,3	K562	blood:
2	chr17:45006845..45009622-chr17:45011752..45014606,5	K562	blood:
3	chr17:45012071..45014988-chr17:45016677..45019422,3	K562	blood:

Variant related genes	Relation type
GOSR2	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1047779	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052504	0.99[ASN][1000 genomes]
rs1052586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853085	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10853087	0.99[ASN][1000 genomes]
rs11079742	0.82[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes]
rs11079745	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079750	0.81[CEU][hapmap]
rs11652318	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11654971	0.99[ASN][1000 genomes]
rs11655668	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11656362	0.97[ASN][1000 genomes]
rs11658276	0.97[ASN][1000 genomes]
rs11869840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601886	0.99[ASN][1000 genomes]
rs12940071	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1618989	0.98[ASN][1000 genomes]
rs1623402	0.99[ASN][1000 genomes]
rs1662576	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1662577	0.99[ASN][1000 genomes]
rs1662594	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662596	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662597	0.96[ASN][1000 genomes]
rs17608961	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1838105	0.82[JPT][hapmap]
rs1867237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs189899	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs197912	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs197913	0.87[ASN][1000 genomes]
rs197915	0.90[ASN][1000 genomes]
rs197917	0.97[ASN][1000 genomes]
rs197918	0.99[ASN][1000 genomes]
rs197919	0.99[ASN][1000 genomes]
rs197922	0.82[JPT][hapmap]
rs197923	0.82[JPT][hapmap]
rs197925	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2003538	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003539	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072317	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2191033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2316330	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2317997	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28553405	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920396	0.99[ASN][1000 genomes]
rs2920397	0.99[ASN][1000 genomes]
rs35707546	0.96[ASN][1000 genomes]
rs3760377	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3785888	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785889	0.81[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs3809854	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851784	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851785	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851787	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4074249	0.80[CEU][hapmap]
rs4381655	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4602097	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968248	0.96[ASN][1000 genomes]
rs4968250	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968285	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968286	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968287	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968288	0.99[ASN][1000 genomes]
rs4968290	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968304	0.80[CEU][hapmap]
rs61671555	0.85[EUR][1000 genomes]
rs62075889	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62075896	0.80[EUR][1000 genomes]
rs6504622	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213526	1.00[ASN][1000 genomes]
rs7216991	0.82[EUR][1000 genomes]
rs7225428	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7342957	0.99[ASN][1000 genomes]
rs736603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740617	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs758391	0.82[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs758392	0.88[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs9303532	0.85[EUR][1000 genomes]
rs9889741	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9893713	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9898527	0.85[EUR][1000 genomes]
rs9898981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901977	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9910899	0.85[EUR][1000 genomes]
rs9911366	0.85[EUR][1000 genomes]
rs9911967	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9912794	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer 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 miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs197926	GOSR2	Cis_1M	lymphoblastoid	RTeQTL
rs197926	C17orf53	cis	parietal	SCAN
rs197926	GOSR2	cis	multi-tissue	Pritchard
rs197926	MYL4	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45001600-45020800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:45002000-45021000	Weak transcription	Fetal Heart	heart
3	chr17:45002800-45020000	Strong transcription	Fetal Muscle Leg	muscle
4	chr17:45004200-45018400	Strong transcription	Primary T cells from cord blood	blood
5	chr17:45004800-45018200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:45005000-45019800	Strong transcription	GM12878-XiMat	blood
7	chr17:45005200-45018000	Strong transcription	Primary B cells from cord blood	blood
8	chr17:45005200-45018800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr17:45005400-45017800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr17:45005400-45018400	Strong transcription	Fetal Stomach	stomach
11	chr17:45005400-45018800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr17:45005600-45018600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr17:45005600-45020200	Strong transcription	Fetal Thymus	thymus
14	chr17:45005800-45019800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr17:45005800-45020000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr17:45006000-45012800	Strong transcription	Hela-S3	cervix
17	chr17:45006000-45018400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:45006200-45018400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr17:45006200-45018400	Strong transcription	Thymus	Thymus
20	chr17:45006200-45020000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:45006400-45014400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr17:45006400-45018000	Strong transcription	Ovary	ovary
23	chr17:45006400-45018400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr17:45006400-45018400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:45006400-45018600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr17:45006600-45014200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
27	chr17:45006600-45014800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr17:45006600-45018200	Strong transcription	Adipose Nuclei	Adipose
29	chr17:45006600-45019000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr17:45006600-45019800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr17:45006800-45013200	Strong transcription	Gastric	stomach
32	chr17:45006800-45013400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:45006800-45014200	Strong transcription	Psoas Muscle	Psoas
34	chr17:45006800-45015200	Strong transcription	Right Ventricle	heart
35	chr17:45006800-45017800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr17:45006800-45018000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr17:45006800-45018000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr17:45006800-45018000	Strong transcription	HepG2	liver
39	chr17:45006800-45018200	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr17:45006800-45018200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:45006800-45018200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr17:45006800-45018200	Strong transcription	Fetal Brain Female	brain
43	chr17:45006800-45018200	Strong transcription	Placenta	Placenta
44	chr17:45006800-45018200	Strong transcription	Pancreas	Pancrea
45	chr17:45006800-45018200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr17:45006800-45018200	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr17:45006800-45018600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr17:45006800-45018800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr17:45006800-45018800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr17:45006800-45019400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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