Variant report

Variant	rs1934584
Chromosome Location	chr1:245971712-245971713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:245958486..245963819-chr1:245964384..245971753,7	K562	blood:
2	chr1:245967776..245970325-chr1:245971274..245973112,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4654285	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6700401	0.84[CHD][hapmap]
rs7517143	0.85[CHD][hapmap]
rs7543518	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007728	chr1:245235174-246156455	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv497871	chr1:245706209-246655353	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534412	chr1:245747724-246655416	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1003594	chr1:245801793-246649329	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1004412	chr1:245830921-246169054	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535385	chr1:245830921-246169054	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998007	chr1:245884759-245989362	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv949722	chr1:245898622-245997919	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1011255	chr1:245913512-246065050	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv468794	chr1:245914284-245999838	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv549520	chr1:245914284-245999838	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv998801	chr1:245924108-246131115	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv535386	chr1:245924108-246131115	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1014841	chr1:245936464-246143222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv535387	chr1:245936464-246143222	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1008786	chr1:245948622-246514454	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv535388	chr1:245948622-246514454	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv468805	chr1:245950642-246229245	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv549521	chr1:245950642-246229245	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
21	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
22	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
23	nsv873405	chr1:245959911-246093644	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv1007095	chr1:245964829-246012247	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv535390	chr1:245964829-246012247	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv1001290	chr1:245966190-246018587	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv535391	chr1:245966190-246018587	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
29	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
30	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
31	nsv526429	chr1:245970550-245979357	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1934584	SCGN	trans	brain	seeQTL
rs1934584	PDZK1	trans	brain	seeQTL
rs1934584	ODZ2	trans	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:245949200-245999600	Weak transcription	Gastric	stomach
2	chr1:245961800-245980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:245962000-245972600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:245964800-245973800	Weak transcription	Fetal Stomach	stomach
5	chr1:245968200-245972600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:245968400-245975200	Weak transcription	Placenta	Placenta
7	chr1:245968400-245985800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:245969600-245974000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:245969600-245975800	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:245969800-245972600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:245970200-245972000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:245970200-245974200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:245970200-245974400	Enhancers	Primary B cells from cord blood	blood
14	chr1:245970400-245971800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:245970400-245971800	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:245970400-245972000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:245970400-245972000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:245970400-245973800	Enhancers	HepG2	liver
19	chr1:245970400-245975400	Enhancers	Fetal Brain Male	brain
20	chr1:245970600-245971800	Enhancers	Fetal Kidney	kidney
21	chr1:245970600-245971800	Enhancers	Fetal Lung	lung
22	chr1:245970600-245971800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:245970600-245978000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:245970800-245971800	Active TSS	Duodenum Mucosa	Duodenum
25	chr1:245970800-245971800	Weak transcription	Ovary	ovary
26	chr1:245970800-245972800	Weak transcription	Spleen	Spleen
27	chr1:245970800-245973600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:245971000-245978600	Weak transcription	K562	blood
29	chr1:245971200-245971800	Enhancers	Fetal Heart	heart
30	chr1:245971200-245972000	Enhancers	Stomach Mucosa	stomach
31	chr1:245971200-245985800	Weak transcription	Osteobl	bone
32	chr1:245971400-245971800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:245971600-245972000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr1:245971600-245972000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:245971600-245972000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:245971600-245972000	Enhancers	Fetal Intestine Small	intestine
37	chr1:245971600-245972000	Enhancers	Fetal Muscle Leg	muscle
38	chr1:245971600-245972400	Weak transcription	Fetal Brain Female	brain
39	chr1:245971600-245972800	Enhancers	Fetal Intestine Large	intestine

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