Variant report

Variant	rs1749405
Chromosome Location	chr1:155860091-155860092
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	NFIC	chr1:155859245-155860540	SK-N-SH	brain:	n/a	n/a
2	GATA2	chr1:155859291-155860153	HUVEC	blood vessel:	n/a	chr1:155859481-155859490

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155824926..155827378-chr1:155859705..155861339,2	K562	blood:

Variant related genes	Relation type
RNU4-19P	TF binding region
ENSG00000116580	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10796955	0.80[CHB][hapmap]
rs11264422	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12024880	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12027412	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12563627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1749410	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1889532	0.80[CHB][hapmap]
rs2993207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3820594	0.80[JPT][hapmap]
rs4661151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4661175	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs4661218	0.80[CHB][hapmap]
rs488079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs490498	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs539602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs639398	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs656247	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs656737	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs670523	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729022	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7517204	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7538214	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs822490	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs822504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs822505	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs822508	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs822509	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs860295	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs928596	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1749405	PRUNE	cis	cerebellum	SCAN
rs1749405	SPRR3	cis	parietal	SCAN
rs1749405	ROBLD3	cis	parietal	SCAN
rs1749405	YY1AP1	cis	cerebellum	SCAN
rs1749405	SLC39A1	cis	cerebellum	SCAN
rs1749405	ADAM15	cis	multi-tissue	Pritchard
rs1749405	RIT1	cis	cerebellum	SCAN
rs1749405	FAM189B	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155830000-155869000	Weak transcription	Gastric	stomach
2	chr1:155830400-155865800	Weak transcription	Esophagus	oesophagus
3	chr1:155830600-155866800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:155831000-155862600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:155831000-155862800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:155831000-155863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:155831200-155862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:155836400-155866400	Weak transcription	Primary B cells from cord blood	blood
9	chr1:155837600-155863000	Weak transcription	Colonic Mucosa	Colon
10	chr1:155841400-155863000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:155841800-155869200	Weak transcription	Right Ventricle	heart
12	chr1:155842600-155863400	Weak transcription	Right Atrium	heart
13	chr1:155844000-155862200	Weak transcription	Lung	lung
14	chr1:155844400-155874000	Weak transcription	Fetal Brain Male	brain
15	chr1:155847000-155860200	Strong transcription	Fetal Brain Female	brain
16	chr1:155847200-155860200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:155847400-155860400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:155847600-155866400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:155849400-155863000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:155849600-155862800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:155850000-155862800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:155850400-155862400	Weak transcription	Placenta	Placenta
23	chr1:155850600-155873600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:155851400-155862600	Weak transcription	Adipose Nuclei	Adipose
25	chr1:155851400-155862600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:155851400-155862800	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:155851400-155863200	Weak transcription	Aorta	Aorta
28	chr1:155851400-155866000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:155851400-155866000	Weak transcription	Spleen	Spleen
30	chr1:155851400-155866400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:155851400-155867400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:155851600-155866800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:155851600-155870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:155852600-155862800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:155852600-155863000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:155853000-155863400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:155853200-155862200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:155853200-155863000	Weak transcription	Left Ventricle	heart
39	chr1:155853600-155862800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:155854200-155862400	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:155854200-155868600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:155854400-155866200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:155854400-155866400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:155854400-155873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:155854800-155862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:155854800-155862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:155854800-155868800	Weak transcription	Ovary	ovary
48	chr1:155855200-155862400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:155855200-155862600	Weak transcription	K562	blood
50	chr1:155855200-155863200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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