Variant report

Variant	rs6951648
Chromosome Location	chr7:50567493-50567494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1037351	0.91[JPT][hapmap];0.92[LWK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs1137337	0.84[AFR][1000 genomes]
rs11575372	0.85[ASN][1000 genomes]
rs11575383	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs11575387	0.81[ASW][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11575388	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11575422	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11575431	0.85[ASN][1000 genomes]
rs11575434	0.88[ASN][1000 genomes]
rs11575438	0.85[AFR][1000 genomes]
rs11575441	0.85[ASN][1000 genomes]
rs11575450	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs17133842	0.90[JPT][hapmap]
rs17133853	0.81[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17152014	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs17152020	0.83[LWK][hapmap];0.95[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs2167364	0.91[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.91[AFR][1000 genomes]
rs2329368	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs3779084	1.00[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4490786	0.80[LWK][hapmap];0.89[MKK][hapmap];0.90[YRI][hapmap]
rs56069386	0.85[AFR][1000 genomes]
rs58024888	0.85[ASN][1000 genomes]
rs58085392	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs59239231	0.85[AFR][1000 genomes]
rs6957607	0.85[AFR][1000 genomes]
rs72645710	0.85[ASN][1000 genomes]
rs7791875	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs880028	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription 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
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv516640	chr7:50565963-50568735	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6951648	ZNFN1A1	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50543600-50595000	Weak transcription	Liver	Liver
2	chr7:50560800-50581000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:50565200-50568600	Weak transcription	Gastric	stomach
4	chr7:50565200-50569800	Weak transcription	Right Atrium	heart
5	chr7:50565200-50570000	Weak transcription	Left Ventricle	heart
6	chr7:50565200-50570200	Weak transcription	Lung	lung
7	chr7:50565200-50572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:50565400-50568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:50565400-50569800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:50565400-50570000	Weak transcription	Pancreas	Pancrea
12	chr7:50565400-50570000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:50565400-50570000	Enhancers	Hela-S3	cervix
14	chr7:50565600-50569800	Weak transcription	Fetal Lung	lung
15	chr7:50565800-50569000	Strong transcription	HepG2	liver
16	chr7:50565800-50570000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:50566000-50569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:50566200-50567600	Weak transcription	Fetal Stomach	stomach
19	chr7:50566200-50568400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:50566200-50568400	Weak transcription	Spleen	Spleen
21	chr7:50566200-50568600	Weak transcription	Psoas Muscle	Psoas
22	chr7:50566200-50569400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:50566200-50569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:50566200-50569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:50566200-50569600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:50566200-50569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:50566200-50569800	Weak transcription	Ovary	ovary
28	chr7:50566200-50576000	Weak transcription	Colonic Mucosa	Colon
29	chr7:50566200-50581200	Strong transcription	Fetal Intestine Small	intestine
30	chr7:50566400-50568800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:50566400-50572600	Strong transcription	Fetal Intestine Large	intestine
32	chr7:50566600-50569800	Weak transcription	HUVEC	blood vessel
33	chr7:50566800-50571400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr7:50567200-50568200	Weak transcription	Fetal Muscle Leg	muscle
35	chr7:50567200-50568800	Weak transcription	HMEC	breast
36	chr7:50567400-50567600	Enhancers	Fetal Muscle Trunk	muscle
37	chr7:50567400-50567600	Enhancers	Stomach Smooth Muscle	stomach

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