Variant report

Variant	rs798938
Chromosome Location	chr7:120741223-120741224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120627916..120631226-chr7:120738829..120742113,4	K562	blood:
2	chr7:120739177..120742283-chr7:120745711..120747787,4	K562	blood:
3	chr7:120624272..120626644-chr7:120740738..120743095,2	K562	blood:
4	chr7:120723287..120725669-chr7:120740976..120742923,2	K562	blood:

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10228942	1.00[JPT][hapmap]
rs1024743	0.91[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10248019	1.00[JPT][hapmap]
rs10268570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11979342	0.82[EUR][1000 genomes]
rs11981613	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11983939	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12706322	0.92[CEU][hapmap]
rs13221538	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs13229354	0.92[CEU][hapmap]
rs13233295	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap]
rs13235373	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13238393	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap]
rs1404267	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs17143194	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17283542	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2160013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2192289	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2402554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2402556	0.86[ASN][1000 genomes]
rs2402561	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2538491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2538492	0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs2721349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2721374	0.86[ASN][1000 genomes]
rs2721375	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2908572	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2908574	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968344	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34269514	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34362455	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34385410	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34638154	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35370706	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35411566	0.81[EUR][1000 genomes]
rs4140913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4144090	0.92[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4593468	0.84[EUR][1000 genomes]
rs6956851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6962260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6970001	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6976513	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73433997	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73436037	0.81[EUR][1000 genomes]
rs759157	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7790569	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798932	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798937	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs798939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798940	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs798942	0.85[EUR][1000 genomes]
rs798944	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798945	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs798947	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798948	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9641653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9690141	0.86[ASN][1000 genomes]
rs9690143	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1030792	chr7:120662815-120917533	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1031282	chr7:120667937-120887301	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv539099	chr7:120667937-120887301	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1019025	chr7:120667937-120918696	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv539100	chr7:120667937-120918696	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv534342	chr7:120667938-120887300	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv889118	chr7:120683751-120800837	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv889119	chr7:120688463-120800837	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv889120	chr7:120691417-120800837	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv428506	chr7:120719434-120891759	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv523626	chr7:120738269-120763212	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs798938	NDUFA5	cis	parietal	SCAN
rs798938	FAM3C	cis	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120711400-120790600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr7:120725800-120744400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:120725800-120761800	Weak transcription	Fetal Stomach	stomach
4	chr7:120727800-120756400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:120728600-120741600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:120731200-120747800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:120733000-120747800	Weak transcription	Spleen	Spleen
8	chr7:120733600-120741600	Weak transcription	Ovary	ovary
9	chr7:120733800-120741600	Weak transcription	Psoas Muscle	Psoas
10	chr7:120734000-120741800	Strong transcription	K562	blood
11	chr7:120735400-120741600	Weak transcription	Aorta	Aorta
12	chr7:120735400-120784000	Weak transcription	Right Ventricle	heart
13	chr7:120737400-120747400	Strong transcription	Liver	Liver
14	chr7:120738000-120742400	Weak transcription	Fetal Kidney	kidney
15	chr7:120738000-120745000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:120738200-120749200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:120738800-120743600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:120739000-120741400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:120739000-120741600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr7:120739200-120742800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:120739600-120746400	Strong transcription	HSMM	muscle
22	chr7:120739800-120742600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:120739800-120742800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr7:120739800-120742800	Strong transcription	NHDF-Ad	bronchial
25	chr7:120739800-120743800	Strong transcription	Adipose Nuclei	Adipose
26	chr7:120740000-120741400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr7:120740000-120741800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:120740000-120742400	Strong transcription	Colon Smooth Muscle	Colon
29	chr7:120740200-120741600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:120740200-120741800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:120740400-120741600	Weak transcription	Left Ventricle	heart
32	chr7:120740400-120741800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr7:120740400-120753000	Weak transcription	Osteobl	bone
34	chr7:120740600-120741400	Weak transcription	NHLF	lung
35	chr7:120740600-120758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:120740800-120745000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:120740800-120786000	Weak transcription	Fetal Lung	lung
38	chr7:120741000-120743800	Strong transcription	HSMMtube	muscle
39	chr7:120741200-120742400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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