Variant report

Variant	rs9846998
Chromosome Location	chr3:158552362-158552363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158546388..158549031-chr3:158549491..158552747,3	K562	blood:
2	chr3:158544882..158547801-chr3:158551051..158553794,3	MCF-7	breast:
3	chr3:158552150..158554007-chr3:158577726..158580202,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MFSD1-2	chr3:158551383-158552986	NONHSAT092952

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1604644	0.80[ASN][1000 genomes]
rs1870829	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364910	0.88[ASN][1000 genomes]
rs35388278	0.85[ASN][1000 genomes]
rs3765083	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680471	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778714	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs6785502	0.85[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs6807246	0.87[ASN][1000 genomes]
rs751834	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs905457	0.84[ASN][1000 genomes]
rs9290029	0.88[ASN][1000 genomes]
rs9839548	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855921	0.80[ASN][1000 genomes]
rs9877166	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active 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	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9846998	LXN	cis	lymphoblastoid	seeQTL
rs9846998	GFM1	cis	cerebellum	SCAN
rs9846998	TIPARP	cis	cerebellum	SCAN
rs9846998	RP11-379F4.9	cis	Thyroid	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158520400-158552400	Weak transcription	Stomach Mucosa	stomach
2	chr3:158527800-158554000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:158532400-158557800	Weak transcription	Gastric	stomach
4	chr3:158533000-158556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:158533000-158559600	Weak transcription	Right Ventricle	heart
6	chr3:158541800-158554200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:158541800-158555000	Weak transcription	Spleen	Spleen
8	chr3:158541800-158560200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:158542000-158556400	Weak transcription	Brain Germinal Matrix	brain
10	chr3:158542200-158561000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:158542400-158553800	Weak transcription	Fetal Brain Female	brain
12	chr3:158542600-158558000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:158543600-158553400	Weak transcription	NHLF	lung
14	chr3:158543600-158555200	Weak transcription	Esophagus	oesophagus
15	chr3:158544000-158556200	Weak transcription	Small Intestine	intestine
16	chr3:158545600-158552400	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:158546400-158565200	Weak transcription	Osteobl	bone
18	chr3:158548600-158553000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:158548600-158554600	Weak transcription	Fetal Lung	lung
20	chr3:158548600-158554800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:158548600-158555400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:158548600-158559000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:158548600-158569400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:158548600-158571200	Weak transcription	Pancreas	Pancrea
25	chr3:158548800-158552400	Weak transcription	Fetal Stomach	stomach
26	chr3:158548800-158553600	Weak transcription	HSMMtube	muscle
27	chr3:158548800-158555000	Weak transcription	Psoas Muscle	Psoas
28	chr3:158548800-158563800	Weak transcription	Brain Anterior Caudate	brain
29	chr3:158548800-158576400	Weak transcription	Left Ventricle	heart
30	chr3:158549800-158564800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:158550000-158552600	Weak transcription	Ovary	ovary
32	chr3:158550000-158553600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:158550200-158552800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:158550200-158586600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:158550600-158552400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:158550600-158552600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:158550600-158553400	Weak transcription	Primary B cells from cord blood	blood
38	chr3:158550600-158554600	Weak transcription	Liver	Liver
39	chr3:158550600-158556800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:158550800-158552400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr3:158550800-158552400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:158550800-158552400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:158550800-158553600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:158550800-158553800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:158550800-158555200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:158550800-158562000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:158550800-158565200	Weak transcription	Primary T cells from cord blood	blood
48	chr3:158551000-158553000	Weak transcription	Adipose Nuclei	Adipose
49	chr3:158551000-158553000	Weak transcription	HSMM	muscle
50	chr3:158551000-158553600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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