Variant report

Variant	rs12673256
Chromosome Location	chr7:21966273-21966274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10950883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128250	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055905	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12055908	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12539984	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919906	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55658106	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57033293	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57082026	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59258063	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62445924	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62445926	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62445928	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62445933	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62445935	0.90[ASN][1000 genomes]
rs6959493	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6959806	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6963571	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6978094	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7798564	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807924	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv275068	chr7:21966107-21980773	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12673256	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 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	chr7:21954800-21970400	Weak transcription	Liver	Liver
6	chr7:21954800-21971800	Weak transcription	Gastric	stomach
7	chr7:21955000-21967400	Weak transcription	Fetal Intestine Small	intestine
8	chr7:21955000-21969800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:21955000-21979000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:21955000-21979200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:21955000-21979600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:21955000-21981000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:21955200-21967800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:21956000-21976400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr7:21956000-21981000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:21956200-21967200	Weak transcription	Thymus	Thymus
17	chr7:21956200-21967400	Weak transcription	Fetal Stomach	stomach
18	chr7:21956200-21976800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:21956400-21980200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:21956600-21966400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:21956600-21967400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:21956600-21970000	Weak transcription	Fetal Thymus	thymus
23	chr7:21956600-21983600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:21956800-21966600	Weak transcription	NHEK	skin
25	chr7:21959800-21967000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:21959800-21973800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr7:21961200-21967600	Weak transcription	Right Ventricle	heart
28	chr7:21961400-21967200	Weak transcription	Primary T cells from cord blood	blood
29	chr7:21962200-21967200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr7:21963200-21967400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr7:21963400-21967400	Weak transcription	Left Ventricle	heart
32	chr7:21963400-21979200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:21963600-21967400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr7:21963600-21968000	Weak transcription	Psoas Muscle	Psoas
35	chr7:21963600-21983600	Weak transcription	Ovary	ovary
36	chr7:21964000-21979200	Weak transcription	Hela-S3	cervix
37	chr7:21964200-21967200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr7:21964200-21967200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr7:21964200-21977400	Weak transcription	HUVEC	blood vessel
40	chr7:21964400-21966600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:21964800-21967000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:21965000-21967000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:21965000-21967200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr7:21965000-21967200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:21965000-21967200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:21965000-21967400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:21965000-21973600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr7:21965000-21976800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr7:21965200-21966400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr7:21965200-21967200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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