Variant report

Variant	rs11789973
Chromosome Location	chr9:94651984-94651985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94650894..94652826-chr9:94665751..94669153,3	K562	blood:
2	chr9:94537420..94538338-chr9:94651419..94651987,2	MCF-7	breast:
3	chr9:94641817..94643317-chr9:94650910..94653000,2	K562	blood:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10761133	0.84[CEU][hapmap]
rs10761134	0.84[CEU][hapmap]
rs10761135	0.84[CEU][hapmap]
rs10761137	0.87[CEU][hapmap]
rs10820908	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992124	0.82[TSI][hapmap]
rs10992129	0.84[CEU][hapmap]
rs10992130	0.84[TSI][hapmap]
rs10992132	0.84[TSI][hapmap]
rs10992137	0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs10992139	0.81[AMR][1000 genomes]
rs10992149	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992158	0.83[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992161	0.82[TSI][hapmap]
rs11792319	0.81[EUR][1000 genomes]
rs12552858	0.80[CEU][hapmap];0.81[AMR][1000 genomes]
rs12555334	0.80[CEU][hapmap]
rs12683797	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1609292	0.87[CEU][hapmap]
rs16907887	0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs1881387	0.80[CHB][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs1881392	0.84[TSI][hapmap]
rs1892263	0.82[TSI][hapmap]
rs2030992	0.82[AMR][1000 genomes]
rs2141368	0.84[TSI][hapmap]
rs3905385	0.91[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4347043	0.81[EUR][1000 genomes]
rs4347044	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4430151	0.96[CEU][hapmap]
rs4517189	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4639579	0.87[TSI][hapmap]
rs4744108	0.81[AMR][1000 genomes]
rs4744109	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744110	0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744112	0.84[CEU][hapmap]
rs4744113	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55864279	0.82[AMR][1000 genomes]
rs57688942	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58431919	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59723153	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62565678	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6479376	0.87[TSI][hapmap]
rs6479383	0.96[CEU][hapmap]
rs67944481	0.82[AMR][1000 genomes]
rs7033819	0.80[CHB][hapmap]
rs72746246	0.84[AMR][1000 genomes]
rs7855417	0.87[TSI][hapmap]
rs7867707	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11789973	NFIL3	cis	lymphoblastoid	seeQTL
rs11789973	SPTLC1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94646000-94652600	Enhancers	Ovary	ovary
2	chr9:94646000-94654800	Enhancers	Fetal Lung	lung
3	chr9:94646600-94654600	Enhancers	Fetal Stomach	stomach
4	chr9:94646600-94658200	Weak transcription	Fetal Heart	heart
5	chr9:94647200-94652600	Enhancers	Fetal Intestine Large	intestine
6	chr9:94647800-94652200	Weak transcription	Brain Substantia Nigra	brain
7	chr9:94648800-94653200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:94648800-94658400	Weak transcription	Pancreas	Pancrea
9	chr9:94648800-94661000	Weak transcription	Spleen	Spleen
10	chr9:94649400-94663200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:94649800-94658400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:94650000-94653400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:94650000-94662400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:94650400-94653600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr9:94650600-94652200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr9:94650600-94654600	Enhancers	Rectal Smooth Muscle	rectum
17	chr9:94650800-94652000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:94650800-94652000	Enhancers	Colonic Mucosa	Colon
19	chr9:94650800-94652000	Enhancers	Lung	lung
20	chr9:94650800-94652000	Enhancers	Right Atrium	heart
21	chr9:94650800-94652600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:94651000-94652200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:94651000-94652400	Bivalent Enhancer	Placenta	Placenta
24	chr9:94651000-94652800	Weak transcription	Fetal Kidney	kidney
25	chr9:94651200-94653200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:94651200-94659200	Enhancers	Colon Smooth Muscle	Colon
27	chr9:94651200-94665000	Weak transcription	NHLF	lung
28	chr9:94651400-94652400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr9:94651600-94652600	Genic enhancers	Fetal Intestine Small	intestine
30	chr9:94651600-94653200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr9:94651600-94653800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:94651600-94656400	Weak transcription	K562	blood
33	chr9:94651600-94660800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:94651800-94652000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:94651800-94652600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:94651800-94659200	Enhancers	Stomach Smooth Muscle	stomach

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