Variant report

Variant	rs3087548
Chromosome Location	chr9:116029174-116029175
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	chr9:116024571..116026114-chr9:116029017..116030804,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC31A1-1	chr9:116028516-116029215	NONHSAT134328

Extended variants
information (count: 31 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10116039	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs10120404	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10123780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125030	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125032	0.90[AFR][1000 genomes]
rs10513190	1.00[CHB][hapmap]
rs10817474	0.86[CEU][hapmap]
rs10981723	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs11789775	0.92[EUR][1000 genomes]
rs11793978	1.00[CHB][hapmap]
rs11794214	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11794663	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12337498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337709	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342489	0.91[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs12350705	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16931988	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs17763351	1.00[CHB][hapmap]
rs17763934	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17764013	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17831500	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2233913	1.00[CHB][hapmap]
rs3088235	0.86[CEU][hapmap]
rs3810917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3810918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3810919	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs41307479	0.81[EUR][1000 genomes]
rs4979229	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3087548	CDC26	cis	cerebellum	SCAN
rs3087548	CDC26	cis	Muscle Skeletal	GTEx
rs3087548	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs3087548	CDC26	cis	Heart Left Ventricle	GTEx
rs3087548	PRPF4	cis	Thyroid	GTEx
rs3087548	CDC26	cis	parietal	SCAN
rs3087548	ZNF483	cis	cerebellum	SCAN
rs3087548	PRPF4	cis	Stomach	GTEx
rs3087548	PRPF4	cis	lung	GTEx
rs3087548	HDHD3	cis	lymphoblastoid	seeQTL
rs3087548	CDC26	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:116009600-116029800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:116010200-116031800	Weak transcription	Fetal Heart	heart
5	chr9:116017600-116031800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:116018600-116036000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:116019600-116033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:116020000-116029600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:116020600-116031600	Weak transcription	HUVEC	blood vessel
10	chr9:116021000-116036000	Strong transcription	Fetal Stomach	stomach
11	chr9:116021200-116031600	Weak transcription	Fetal Brain Male	brain
12	chr9:116021200-116032200	Weak transcription	Small Intestine	intestine
13	chr9:116021200-116032600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:116021400-116029800	Weak transcription	Primary B cells from cord blood	blood
15	chr9:116021400-116032200	Weak transcription	Pancreas	Pancrea
16	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
17	chr9:116022600-116029400	Weak transcription	NH-A	brain
18	chr9:116022600-116031600	Weak transcription	NHDF-Ad	bronchial
19	chr9:116022800-116030200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:116022800-116030600	Weak transcription	K562	blood
21	chr9:116022800-116031600	Weak transcription	Psoas Muscle	Psoas
22	chr9:116022800-116031800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:116022800-116032200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:116022800-116032200	Weak transcription	Esophagus	oesophagus
25	chr9:116022800-116036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:116023000-116029800	Weak transcription	Thymus	Thymus
27	chr9:116023000-116029800	Weak transcription	Spleen	Spleen
28	chr9:116023000-116031400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:116023000-116031800	Weak transcription	NHLF	lung
30	chr9:116023000-116032200	Weak transcription	Gastric	stomach
31	chr9:116023000-116033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:116023000-116033200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:116023200-116031600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:116023200-116031800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr9:116023200-116031800	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:116023400-116030200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:116023400-116032200	Weak transcription	Right Ventricle	heart
39	chr9:116023400-116034200	Weak transcription	Colonic Mucosa	Colon
40	chr9:116023600-116032200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:116024200-116030800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:116024600-116030400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:116024600-116031600	Weak transcription	Hela-S3	cervix
44	chr9:116024800-116029800	Weak transcription	Brain Substantia Nigra	brain
45	chr9:116024800-116029800	Weak transcription	Osteobl	bone
46	chr9:116024800-116030200	Weak transcription	Ovary	ovary
47	chr9:116024800-116030400	Weak transcription	GM12878-XiMat	blood
48	chr9:116024800-116030800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr9:116024800-116031800	Weak transcription	HSMMtube	muscle
50	chr9:116024800-116032200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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