Variant report

Variant	rs12700327
Chromosome Location	chr7:21955785-21955786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs4398800	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4566940	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60181879	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6651057	0.81[TSI][hapmap]
rs6978094	0.83[ASW][hapmap]
rs7807075	0.81[TSI][hapmap]
rs7807924	0.83[ASW][hapmap];0.88[YRI][hapmap]

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	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12700327	C7orf46	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21933000-21963200	Weak transcription	A549	lung
2	chr7:21936600-21956400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr7:21936600-21956600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:21937000-21956400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:21937200-21956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:21937400-21956000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:21937600-21956200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:21937600-21956400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:21937800-21956000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr7:21937800-21956200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:21938000-21956200	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr7:21938800-21956600	Strong transcription	Primary T cells from cord blood	blood
14	chr7:21942400-21957200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:21944000-21957400	Weak transcription	Colonic Mucosa	Colon
16	chr7:21944200-21956200	Weak transcription	Spleen	Spleen
17	chr7:21944400-21956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:21946000-21956200	Weak transcription	Brain Substantia Nigra	brain
19	chr7:21946000-21956400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr7:21946200-21957600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:21946200-21963400	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:21947800-21956000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr7:21947800-21958000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:21948200-21956400	Weak transcription	Fetal Intestine Large	intestine
25	chr7:21948400-21956400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:21948400-21960400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr7:21948800-21981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:21949800-21955800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:21950400-21960400	Weak transcription	Fetal Brain Female	brain
30	chr7:21950800-21956600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:21951400-21955800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr7:21951600-21982600	Weak transcription	HSMM	muscle
33	chr7:21952000-21956200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:21952400-21956200	Strong transcription	Fetal Stomach	stomach
35	chr7:21952400-21963200	Weak transcription	Psoas Muscle	Psoas
36	chr7:21952600-21958400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:21952600-21977400	Weak transcription	NHDF-Ad	bronchial
38	chr7:21952800-21955800	Weak transcription	Osteobl	bone
39	chr7:21952800-21956000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:21952800-21960000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:21952800-21963200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:21953000-21956400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:21953200-21955800	Strong transcription	Lung	lung
44	chr7:21953200-21956000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr7:21953200-21956000	Strong transcription	Fetal Muscle Leg	muscle
46	chr7:21953400-21956200	Strong transcription	Thymus	Thymus
47	chr7:21953400-21956400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:21953400-21956400	Strong transcription	Fetal Lung	lung
49	chr7:21953400-21960200	Weak transcription	Brain Germinal Matrix	brain
50	chr7:21953600-21956600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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