Variant report

Variant	rs1346834
Chromosome Location	chr3:158490420-158490421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158439811..158443418-chr3:158489187..158492099,4	MCF-7	breast:
2	chr3:158439870..158442548-chr3:158488402..158491335,2	MCF-7	breast:
3	chr3:158485915..158488548-chr3:158489974..158493144,3	MCF-7	breast:
4	chr3:158486291..158488214-chr3:158488282..158491232,3	K562	blood:
5	chr3:158489358..158491459-chr3:158497212..158500197,2	MCF-7	breast:
6	chr3:158483650..158485316-chr3:158488021..158490619,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1006911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864508	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2115941	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2253249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs2364927	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2566346	0.80[ASN][1000 genomes]
rs2615052	0.98[ASN][1000 genomes]
rs4680460	0.80[CHB][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs4680467	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57932243	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61794797	0.80[ASN][1000 genomes]
rs6441224	0.91[ASN][1000 genomes]
rs6441225	0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6802315	0.98[ASN][1000 genomes]
rs6804249	0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs7615751	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7618110	0.90[ASN][1000 genomes]
rs7635993	0.93[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9822005	0.86[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9861938	0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9863103	1.00[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9866134	0.80[ASN][1000 genomes]
rs9881462	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1346834	LXN	cis	parietal	SCAN
rs1346834	LXN	cis	cerebellum	SCAN
rs1346834	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs1346834	RP11-379F4.9	cis	Thyroid	GTEx
rs1346834	LXN	cis	lymphoblastoid	seeQTL
rs1346834	MLF1	cis	Heart Left Ventricle	GTEx
rs1346834	RARRES1	cis	cerebellum	SCAN
rs1346834	GFM1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158479600-158495600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:158482800-158490600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:158483400-158490600	Enhancers	HMEC	breast
4	chr3:158485600-158490600	Enhancers	Placenta	Placenta
5	chr3:158485600-158495800	Enhancers	Fetal Intestine Small	intestine
6	chr3:158486400-158494200	Weak transcription	Gastric	stomach
7	chr3:158486600-158491000	Enhancers	K562	blood
8	chr3:158486600-158494200	Weak transcription	Pancreas	Pancrea
9	chr3:158486800-158518200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:158487000-158491800	Weak transcription	Fetal Brain Male	brain
11	chr3:158487400-158496600	Enhancers	Fetal Lung	lung
12	chr3:158488400-158490600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:158488400-158492000	Weak transcription	Aorta	Aorta
14	chr3:158488400-158493400	Weak transcription	Lung	lung
15	chr3:158488400-158493600	Weak transcription	Left Ventricle	heart
16	chr3:158488400-158501000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:158488600-158491000	Weak transcription	Fetal Kidney	kidney
18	chr3:158488600-158491400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:158488800-158494400	Weak transcription	Osteobl	bone
20	chr3:158489200-158495000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:158489200-158508800	Weak transcription	Primary T cells from cord blood	blood
22	chr3:158489400-158491200	Weak transcription	NHLF	lung
23	chr3:158489400-158492800	Enhancers	Fetal Intestine Large	intestine
24	chr3:158489600-158490600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr3:158489800-158491000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:158489800-158491400	Weak transcription	Fetal Stomach	stomach
27	chr3:158489800-158494400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:158489800-158495200	Weak transcription	Colonic Mucosa	Colon
29	chr3:158489800-158495200	Weak transcription	Small Intestine	intestine
30	chr3:158489800-158500600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:158490000-158491200	Weak transcription	Adipose Nuclei	Adipose
32	chr3:158490000-158501000	Weak transcription	Ovary	ovary
33	chr3:158490200-158490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:158490200-158491200	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:158490200-158491200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:158490200-158492000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:158490200-158493200	Weak transcription	HepG2	liver
38	chr3:158490200-158497800	Weak transcription	Hela-S3	cervix
39	chr3:158490400-158491400	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:158490400-158491600	Weak transcription	A549	lung
41	chr3:158490400-158494200	Weak transcription	Right Atrium	heart

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