Variant report

Variant	rs1870829
Chromosome Location	chr3:158554978-158554979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158552403..158553952-chr3:158554364..158557250,2	K562	blood:
2	chr3:158553808..158556556-chr3:158560756..158562852,2	K562	blood:
3	chr3:158554664..158556817-chr3:158563538..158566180,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2364910	0.86[ASN][1000 genomes]
rs35388278	0.84[ASN][1000 genomes]
rs3765083	0.94[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680470	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680471	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6778714	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs6785502	0.80[CHB][hapmap];0.84[CHD][hapmap]
rs6807246	0.84[ASN][1000 genomes]
rs751834	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs905457	0.83[ASN][1000 genomes]
rs9290029	0.86[ASN][1000 genomes]
rs9839548	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846998	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877166	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
16	nsv1014021	chr3:158554615-158635122	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv592124	chr3:158554978-158636057	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1870829	GFM1	cis	cerebellum	SCAN
rs1870829	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs1870829	RP11-379F4.9	cis	Thyroid	GTEx
rs1870829	TIPARP	cis	cerebellum	SCAN
rs1870829	LXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158532400-158557800	Weak transcription	Gastric	stomach
2	chr3:158533000-158556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:158533000-158559600	Weak transcription	Right Ventricle	heart
4	chr3:158541800-158555000	Weak transcription	Spleen	Spleen
5	chr3:158541800-158560200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:158542000-158556400	Weak transcription	Brain Germinal Matrix	brain
7	chr3:158542200-158561000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:158542600-158558000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:158543600-158555200	Weak transcription	Esophagus	oesophagus
10	chr3:158544000-158556200	Weak transcription	Small Intestine	intestine
11	chr3:158546400-158565200	Weak transcription	Osteobl	bone
12	chr3:158548600-158555400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:158548600-158559000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:158548600-158569400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:158548600-158571200	Weak transcription	Pancreas	Pancrea
16	chr3:158548800-158555000	Weak transcription	Psoas Muscle	Psoas
17	chr3:158548800-158563800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:158548800-158576400	Weak transcription	Left Ventricle	heart
19	chr3:158549800-158564800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:158550200-158586600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:158550600-158556800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:158550800-158555200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:158550800-158562000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:158550800-158565200	Weak transcription	Primary T cells from cord blood	blood
25	chr3:158551000-158559000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:158551000-158565400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:158551200-158561000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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