Variant report

Variant	rs4727922
Chromosome Location	chr7:120987119-120987120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120986190..120988228-chr7:120994808..120997127,2	K562	blood:
2	chr7:120985694..120988582-chr7:121034968..121037690,2	K562	blood:
3	chr7:120969341..120972493-chr7:120983934..120987124,3	K562	blood:
4	chr7:120983315..120988204-chr7:120988665..120992990,4	K562	blood:
5	chr7:120986514..120988204-chr7:120990711..120992990,2	K562	blood:

Variant related genes	Relation type
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10250624	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs10250907	0.84[EUR][1000 genomes]
rs11762263	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11762452	0.86[EUR][1000 genomes]
rs11768996	0.93[CEU][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs11770098	0.84[EUR][1000 genomes]
rs11771477	0.84[EUR][1000 genomes]
rs12706336	0.84[EUR][1000 genomes]
rs12706337	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs12706338	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12706339	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12706340	0.85[EUR][1000 genomes]
rs12706341	0.93[CEU][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs12706342	0.83[EUR][1000 genomes]
rs12706343	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12706346	1.00[CHD][hapmap]
rs13232217	0.97[AMR][1000 genomes]
rs13232320	0.97[AMR][1000 genomes]
rs13238085	0.85[EUR][1000 genomes]
rs17143305	0.85[EUR][1000 genomes]
rs1803389	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1990446	0.93[CEU][hapmap];0.81[MEX][hapmap]
rs1990447	0.84[EUR][1000 genomes]
rs2041490	0.85[CEU][hapmap]
rs2254591	0.84[EUR][1000 genomes]
rs2536153	0.85[EUR][1000 genomes]
rs2536155	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs2536156	0.84[EUR][1000 genomes]
rs2536157	0.83[EUR][1000 genomes]
rs2536158	0.84[EUR][1000 genomes]
rs2536159	0.84[EUR][1000 genomes]
rs2536160	0.84[EUR][1000 genomes]
rs2536163	0.93[CEU][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs2536164	0.84[EUR][1000 genomes]
rs2536165	0.93[CEU][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs2536166	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs2536167	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs2536168	0.84[EUR][1000 genomes]
rs2536170	0.84[EUR][1000 genomes]
rs2536173	0.84[EUR][1000 genomes]
rs2536174	0.84[EUR][1000 genomes]
rs2536175	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2536176	0.84[EUR][1000 genomes]
rs2536178	0.84[EUR][1000 genomes]
rs2536179	0.84[EUR][1000 genomes]
rs2536184	0.84[EUR][1000 genomes]
rs2536192	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2707460	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs2707461	0.93[CEU][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs2707462	0.84[EUR][1000 genomes]
rs2707463	0.84[EUR][1000 genomes]
rs2707465	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs2707467	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs2707468	0.85[EUR][1000 genomes]
rs2707471	0.92[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2707473	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs2707474	0.85[CEU][hapmap]
rs2707475	0.84[EUR][1000 genomes]
rs2707476	0.84[EUR][1000 genomes]
rs2707477	0.84[EUR][1000 genomes]
rs2707478	0.84[EUR][1000 genomes]
rs2707479	0.93[CEU][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs2707480	0.84[EUR][1000 genomes]
rs2707481	0.83[EUR][1000 genomes]
rs2707482	0.84[EUR][1000 genomes]
rs2707491	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2707492	0.84[EUR][1000 genomes]
rs2707496	0.93[CEU][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs2707504	0.84[EUR][1000 genomes]
rs2707505	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2707507	0.93[CEU][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs2707522	0.85[EUR][1000 genomes]
rs2952564	0.85[EUR][1000 genomes]
rs4727925	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4731011	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71571022	0.86[EUR][1000 genomes]
rs7792993	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs997782	0.93[CEU][hapmap];0.84[EUR][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	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
2	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv2757237	chr7:120908459-120993326	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv2759558	chr7:120908459-120993326	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4727922	FAM3C	cis	lymphoblastoid	seeQTL
rs4727922	HYAL4	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120970600-121016800	Weak transcription	Gastric	stomach
2	chr7:120970600-121025400	Weak transcription	Spleen	Spleen
3	chr7:120970800-121000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:120972000-120992400	Weak transcription	Esophagus	oesophagus
5	chr7:120973800-120998800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:120975600-120992400	Weak transcription	HSMMtube	muscle
7	chr7:120977600-120992400	Weak transcription	Fetal Intestine Small	intestine
8	chr7:120977800-120999800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:120978600-120990600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr7:120978600-120994600	Weak transcription	Fetal Thymus	thymus
11	chr7:120978800-121017400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr7:120979400-120990400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:120979400-120992400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:120979400-120992400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:120979400-120992400	Weak transcription	Lung	lung
16	chr7:120979400-120995400	Weak transcription	Fetal Heart	heart
17	chr7:120979600-120992400	Weak transcription	Aorta	Aorta
18	chr7:120979800-121019400	Weak transcription	Thymus	Thymus
19	chr7:120979800-121034800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:120980000-120992000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:120980400-120987200	Weak transcription	GM12878-XiMat	blood
22	chr7:120980400-120992400	Weak transcription	Fetal Stomach	stomach
23	chr7:120980400-120992600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:120980600-120990600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:120980800-121019600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:120981000-120992400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr7:120981000-121015200	Weak transcription	Pancreas	Pancrea
28	chr7:120981200-120990800	Weak transcription	Placenta	Placenta
29	chr7:120982000-120987800	Strong transcription	Primary B cells from cord blood	blood
30	chr7:120983000-120996600	Weak transcription	Fetal Lung	lung
31	chr7:120983000-121009600	Weak transcription	Hela-S3	cervix
32	chr7:120983200-120992400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:120983600-120992600	Weak transcription	HUVEC	blood vessel
34	chr7:120983800-120994400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:120983800-121000200	Weak transcription	Fetal Kidney	kidney
36	chr7:120984000-120993200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr7:120984000-121017600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:120984200-120990600	Weak transcription	Liver	Liver
39	chr7:120984200-121001200	Weak transcription	NHLF	lung
40	chr7:120984200-121009800	Weak transcription	Fetal Brain Male	brain
41	chr7:120984200-121035000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:120984800-120994600	Weak transcription	Brain Angular Gyrus	brain
43	chr7:120984800-121009600	Weak transcription	A549	lung
44	chr7:120985000-120990600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:120985000-120990600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr7:120985000-120992000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:120985000-120992400	Weak transcription	Brain Germinal Matrix	brain
48	chr7:120985000-120995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:120985000-120995800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr7:120985000-121001200	Weak transcription	Brain Hippocampus Middle	brain

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