Variant report

Variant	rs1870676
Chromosome Location	chr1:72744996-72744997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11584542	0.88[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs11584611	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12137231	0.85[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12137936	0.84[ASN][1000 genomes]
rs1380995	0.84[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1460947	0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1460948	0.88[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs17525824	0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs17591264	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1776012	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1841497	0.84[ASN][1000 genomes]
rs1841500	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2000228	0.88[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2568958	0.84[GIH][hapmap]
rs3101336	0.84[GIH][hapmap]
rs3101340	0.89[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3101341	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7549792	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326098	0.88[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs9424976	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs9424977	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9424978	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9425081	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428454	chr1:72504469-72926256	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1013250	chr1:72603540-72762582	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv830192	chr1:72616562-72806118	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1014832	chr1:72642420-72823477	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv534997	chr1:72642420-72823477	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1835472	chr1:72720026-72820015	Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1008754	chr1:72733738-72763358	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
8	nsv1376	chr1:72734578-72823386	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv254	chr1:72734991-72823194	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv1826553	chr1:72738721-72763358	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
11	nsv1002724	chr1:72738857-72763358	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
12	nsv1013213	chr1:72739953-72802492	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv1014214	chr1:72740734-72808756	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv1010247	chr1:72740734-72809419	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv1002360	chr1:72740734-72809830	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv1007840	chr1:72740734-72810926	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv998364	chr1:72740734-72811136	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv1007101	chr1:72740734-72812440	Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv1011285	chr1:72740734-72818878	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	esv2757734	chr1:72742396-72886813	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	esv2758939	chr1:72742396-72886813	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	esv3491557	chr1:72742853-72851634	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	esv3491558	chr1:72742853-72851634	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1870676	LRRC7	cis	parietal	SCAN
rs1870676	RP11-292O17.1	cis	Thyroid	GTEx
rs1870676	ASB17	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72738000-72745800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:72742800-72745800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:72743000-72745000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:72743000-72745000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:72743000-72745800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:72743600-72745800	Enhancers	Dnd41	blood
7	chr1:72743800-72751600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr1:72744000-72745000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:72744000-72745200	Enhancers	Brain Substantia Nigra	brain
10	chr1:72744200-72745400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:72744200-72745800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:72744200-72746000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:72744400-72745000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:72744400-72745800	Weak transcription	NHDF-Ad	bronchial
15	chr1:72744400-72746400	Enhancers	Rectal Smooth Muscle	rectum
16	chr1:72744600-72745200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:72744600-72745600	Enhancers	Osteobl	bone
18	chr1:72744600-72745800	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr1:72744800-72745000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:72744800-72745000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:72744800-72745000	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr1:72744800-72745000	Enhancers	NHLF	lung
23	chr1:72744800-72745200	Flanking Active TSS	HUVEC	blood vessel
24	chr1:72744800-72746000	Enhancers	HSMM	muscle

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