Variant report

Variant	rs313823
Chromosome Location	chr7:65581996-65581997
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65555345..65557096-chr7:65580124..65582089,2	K562	blood:
2	chr7:65580634..65584487-chr7:65590516..65592938,4	K562	blood:
3	chr7:65581679..65583399-chr7:65586176..65588368,2	MCF-7	breast:
4	chr7:65579988..65582211-chr7:65582533..65585744,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10950024	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10950025	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10950027	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10950028	0.82[EUR][1000 genomes]
rs10950029	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11760805	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11767833	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12666485	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12671834	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12673308	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs160636	0.83[ASN][1000 genomes]
rs160640	0.87[EUR][1000 genomes]
rs160641	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160645	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs160647	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17138089	0.91[ASN][1000 genomes]
rs17138149	0.87[ASN][1000 genomes]
rs221986	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244226	0.85[EUR][1000 genomes]
rs2451953	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460427	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2465121	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28815324	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2946580	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs313817	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs313818	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313828	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs313830	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs313834	0.81[ASN][1000 genomes]
rs316305	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316306	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316316	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316320	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316323	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316324	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316328	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs400767	0.90[ASN][1000 genomes]
rs4441996	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718325	0.87[ASN][1000 genomes]
rs6460276	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6460281	0.89[ASN][1000 genomes]
rs67302640	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67397473	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67688847	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67775320	0.85[ASN][1000 genomes]
rs6960870	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73136346	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73142233	0.88[ASN][1000 genomes]
rs73142245	0.87[ASN][1000 genomes]
rs73142265	0.81[ASN][1000 genomes]
rs73376394	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73376401	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73378304	0.81[EUR][1000 genomes]
rs7782212	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7783727	0.82[ASN][1000 genomes]
rs7786728	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7786735	0.86[ASN][1000 genomes]
rs7787063	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs313823	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs313823	GS1-124K5.4	cis	Stomach	GTEx
rs313823	GS1-124K5.11	cis	Thyroid	GTEx
rs313823	GS1-124K5.4	cis	Artery Aorta	GTEx
rs313823	GTF2IRD1P1	cis	Thyroid	GTEx
rs313823	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs313823	RNU6-96P	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65580600-65582000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:65580600-65583200	Enhancers	Spleen	Spleen
3	chr7:65580600-65583400	Enhancers	Stomach Mucosa	stomach
4	chr7:65580600-65584600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:65580600-65584600	Enhancers	Gastric	stomach
6	chr7:65580600-65591000	Weak transcription	Ovary	ovary
7	chr7:65580600-65600600	Weak transcription	Aorta	Aorta
8	chr7:65580800-65582000	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr7:65580800-65582000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr7:65580800-65582000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr7:65580800-65582200	Flanking Active TSS	GM12878-XiMat	blood
12	chr7:65580800-65582600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr7:65580800-65583200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:65580800-65583800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:65580800-65584200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr7:65580800-65606800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:65581000-65582000	Enhancers	Primary T cells from cord blood	blood
18	chr7:65581000-65582000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:65581000-65582200	Enhancers	Pancreas	Pancrea
20	chr7:65581000-65582400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:65581000-65582400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr7:65581000-65582400	Enhancers	Brain Hippocampus Middle	brain
23	chr7:65581000-65582400	Enhancers	Esophagus	oesophagus
24	chr7:65581000-65582400	Genic enhancers	Fetal Brain Male	brain
25	chr7:65581000-65582400	Enhancers	NHDF-Ad	bronchial
26	chr7:65581000-65582800	Weak transcription	Right Ventricle	heart
27	chr7:65581000-65583000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr7:65581000-65583000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr7:65581000-65583000	Enhancers	Fetal Heart	heart
30	chr7:65581000-65583200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:65581000-65583200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:65581000-65583600	Weak transcription	Brain Substantia Nigra	brain
33	chr7:65581000-65583800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr7:65581000-65584000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:65581000-65584000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr7:65581000-65584000	Weak transcription	Right Atrium	heart
37	chr7:65581000-65584200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:65581000-65584200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:65581000-65584400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr7:65581000-65584600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr7:65581000-65587400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:65581000-65589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr7:65581000-65595600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr7:65581000-65595600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:65581000-65595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:65581000-65597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:65581000-65617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:65581200-65582000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:65581200-65582000	Enhancers	Psoas Muscle	Psoas
50	chr7:65581200-65582200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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