Variant report

Variant	rs12489730
Chromosome Location	chr3:158457914-158457915
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10513528	0.86[YRI][hapmap]
rs12491877	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12495962	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12497488	0.98[ASN][1000 genomes]
rs1430413	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1430414	0.98[ASN][1000 genomes]
rs1560417	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1560418	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16829365	0.89[ASN][1000 genomes]
rs17642769	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17643171	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17643252	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643483	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643581	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643860	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17643917	0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs17699324	0.83[CHD][hapmap];0.96[GIH][hapmap]
rs17699478	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17699526	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17699997	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17700122	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700475	0.98[ASN][1000 genomes]
rs2279561	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279562	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307064	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2566347	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs34690420	0.98[ASN][1000 genomes]
rs3863076	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3867391	0.83[CHD][hapmap];0.96[GIH][hapmap]
rs41434057	0.87[ASW][hapmap];0.86[YRI][hapmap]
rs55678388	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55705231	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs55717824	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55776609	0.91[ASN][1000 genomes]
rs56023805	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56078503	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56105525	0.98[ASN][1000 genomes]
rs56152025	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56235582	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56261306	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56318834	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57262841	0.98[ASN][1000 genomes]
rs59163359	0.98[ASN][1000 genomes]
rs59173444	0.91[ASN][1000 genomes]
rs60203196	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61138408	0.98[ASN][1000 genomes]
rs61794798	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794799	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794818	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794821	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794822	0.98[ASN][1000 genomes]
rs61794833	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794834	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794835	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61794858	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794859	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61796760	0.83[ASN][1000 genomes]
rs61796762	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61796764	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61796766	0.82[ASN][1000 genomes]
rs61796768	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61796770	0.97[ASN][1000 genomes]
rs6441208	0.83[CHD][hapmap];0.88[GIH][hapmap]
rs6441221	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761989	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6783610	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792908	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6804230	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs73158361	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7610009	0.83[CHD][hapmap];0.96[GIH][hapmap]
rs7624420	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7624702	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12489730	LXN	cis	lymphoblastoid	seeQTL
rs12489730	TIPARP	cis	cerebellum	SCAN
rs12489730	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs12489730	IL12A	cis	parietal	SCAN
rs12489730	LXN	cis	cerebellum	SCAN
rs12489730	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs12489730	GFM1	cis	parietal	SCAN
rs12489730	GFM1	cis	Thyroid	GTEx
rs12489730	GFM1	cis	cerebellum	SCAN
rs12489730	LXN	cis	parietal	SCAN
rs12489730	LXN	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450400-158460000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:158450600-158465400	Weak transcription	Left Ventricle	heart
4	chr3:158450800-158460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:158450800-158464200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:158450800-158468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
8	chr3:158451000-158458800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:158451000-158459800	Weak transcription	Fetal Brain Male	brain
10	chr3:158451000-158459800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:158451000-158460000	Weak transcription	Fetal Intestine Large	intestine
12	chr3:158451000-158462000	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:158451000-158463400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:158451000-158463800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:158451000-158464000	Weak transcription	Colonic Mucosa	Colon
16	chr3:158451000-158464400	Weak transcription	NH-A	brain
17	chr3:158451000-158464800	Weak transcription	Gastric	stomach
18	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
20	chr3:158451800-158461400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:158451800-158464800	Weak transcription	Brain Germinal Matrix	brain
22	chr3:158452200-158465600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:158453200-158458200	Weak transcription	Brain Angular Gyrus	brain
24	chr3:158453200-158458800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:158453200-158459800	Weak transcription	Ovary	ovary
26	chr3:158453200-158462000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:158453200-158464600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:158453400-158459400	Weak transcription	Adipose Nuclei	Adipose
29	chr3:158453400-158460800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr3:158453400-158462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:158453400-158464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:158453400-158464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:158453400-158465800	Weak transcription	Fetal Brain Female	brain
34	chr3:158453400-158467400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:158453400-158467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:158453600-158459600	Weak transcription	Primary T cells from cord blood	blood
37	chr3:158453600-158462000	Weak transcription	Brain Anterior Caudate	brain
38	chr3:158453600-158462600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:158453600-158464000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:158453600-158465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:158453600-158486400	Weak transcription	Esophagus	oesophagus
42	chr3:158454000-158460800	Weak transcription	A549	lung
43	chr3:158455400-158465800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:158455800-158460800	Strong transcription	Fetal Stomach	stomach
45	chr3:158456200-158459400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:158456400-158458000	Strong transcription	Fetal Intestine Small	intestine
47	chr3:158456400-158460400	Weak transcription	Placenta	Placenta
48	chr3:158456400-158461600	Weak transcription	Osteobl	bone
49	chr3:158456600-158459800	Weak transcription	Liver	Liver
50	chr3:158456800-158464800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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