Variant report

Variant	rs6948377
Chromosome Location	chr7:140584262-140584263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10247116	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10251628	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10269699	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1267600	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1267601	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1267606	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1267619	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1267620	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17161737	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17161750	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17161767	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2365097	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2365098	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2535947	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28579189	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6464121	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6464123	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6464149	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6967652	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6970121	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975596	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73497923	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73497924	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73502717	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73502740	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73502747	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73502785	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73502799	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7787206	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9655610	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351231	chr7:140390303-140588539	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv831158	chr7:140392222-140602315	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv518139	chr7:140512661-140622355	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1029363	chr7:140567136-140594073	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	esv2761117	chr7:140582100-140594085	Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6948377	JHDM1D,LOC100127997	cis	occipital cortex	BrainEAC

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140549000-140594400	Weak transcription	Fetal Thymus	thymus
2	chr7:140563600-140586000	Weak transcription	K562	blood
3	chr7:140568000-140586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:140570600-140606000	Weak transcription	Fetal Intestine Small	intestine
5	chr7:140573600-140587800	Weak transcription	Left Ventricle	heart
6	chr7:140576600-140585600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:140577000-140586800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:140577000-140591000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:140577400-140585600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:140577600-140586400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr7:140577600-140589600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:140577600-140598600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:140578600-140585600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:140578800-140586200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:140580400-140603200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:140581400-140585600	Weak transcription	Brain Hippocampus Middle	brain
17	chr7:140581400-140587400	Weak transcription	Lung	lung
18	chr7:140581600-140585800	Weak transcription	Primary T cells from cord blood	blood
19	chr7:140581600-140586000	Weak transcription	Brain Angular Gyrus	brain
20	chr7:140581800-140585600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:140581800-140585600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:140581800-140585800	Weak transcription	Brain Anterior Caudate	brain
23	chr7:140581800-140586000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:140581800-140587200	Weak transcription	Fetal Heart	heart
25	chr7:140581800-140588000	Weak transcription	Pancreas	Pancrea
26	chr7:140582000-140585200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:140582600-140599600	Weak transcription	Gastric	stomach
28	chr7:140583600-140585800	Weak transcription	Primary B cells from cord blood	blood
29	chr7:140584000-140585200	Weak transcription	GM12878-XiMat	blood
30	chr7:140584000-140589600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:140584200-140585600	Weak transcription	Primary B cells from peripheral blood	blood

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