Variant report

Variant	rs7798564
Chromosome Location	chr7:21965073-21965074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10950883	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055905	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12055908	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12539984	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673256	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919906	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55658106	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57033293	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57082026	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59258063	0.89[EUR][1000 genomes]
rs62445924	0.86[EUR][1000 genomes]
rs62445926	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62445928	0.89[EUR][1000 genomes]
rs62445933	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62445935	0.90[ASN][1000 genomes]
rs6959493	0.89[EUR][1000 genomes]
rs6959806	0.89[EUR][1000 genomes]
rs6963571	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6978094	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs7807924	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh 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
2	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7798564	C7orf46	cis	parietal	SCAN
rs7798564	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL
rs7798564	CDCA7L	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:21948800-21981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:21951600-21982600	Weak transcription	HSMM	muscle
4	chr7:21952600-21977400	Weak transcription	NHDF-Ad	bronchial
5	chr7:21954800-21966200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:21954800-21970400	Weak transcription	Liver	Liver
7	chr7:21954800-21971800	Weak transcription	Gastric	stomach
8	chr7:21955000-21967400	Weak transcription	Fetal Intestine Small	intestine
9	chr7:21955000-21969800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:21955000-21979000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:21955000-21979200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:21955000-21979600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:21955000-21981000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:21955200-21967800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr7:21956000-21966200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:21956000-21976400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:21956000-21981000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:21956200-21967200	Weak transcription	Thymus	Thymus
19	chr7:21956200-21967400	Weak transcription	Fetal Stomach	stomach
20	chr7:21956200-21976800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:21956400-21965400	Enhancers	Fetal Heart	heart
22	chr7:21956400-21980200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:21956600-21966400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:21956600-21967400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:21956600-21970000	Weak transcription	Fetal Thymus	thymus
26	chr7:21956600-21983600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:21956800-21966600	Weak transcription	NHEK	skin
28	chr7:21958200-21965200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr7:21959600-21965200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:21959800-21967000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr7:21959800-21973800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:21960200-21965200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr7:21961200-21967600	Weak transcription	Right Ventricle	heart
34	chr7:21961400-21967200	Weak transcription	Primary T cells from cord blood	blood
35	chr7:21961600-21966200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:21962200-21967200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:21962800-21965200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:21963200-21967400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr7:21963400-21967400	Weak transcription	Left Ventricle	heart
40	chr7:21963400-21979200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:21963600-21967400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr7:21963600-21968000	Weak transcription	Psoas Muscle	Psoas
43	chr7:21963600-21983600	Weak transcription	Ovary	ovary
44	chr7:21963800-21965200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:21964000-21979200	Weak transcription	Hela-S3	cervix
46	chr7:21964200-21967200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr7:21964200-21967200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr7:21964200-21977400	Weak transcription	HUVEC	blood vessel
49	chr7:21964400-21966600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr7:21964600-21965200	Weak transcription	H9 Cell Line	embryonic stem cell

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