Variant report

Variant	rs6702666
Chromosome Location	chr1:93609843-93609844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93609299..93611965-chr1:93618849..93621976,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11164869	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12062154	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12080248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12736775	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391228	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2749734	0.84[ASN][1000 genomes]
rs2785602	0.89[ASN][1000 genomes]
rs2785605	0.89[ASN][1000 genomes]
rs2815419	0.86[ASN][1000 genomes]
rs2815423	0.89[ASN][1000 genomes]
rs2815424	0.89[ASN][1000 genomes]
rs488345	0.89[ASN][1000 genomes]
rs490153	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs495580	0.89[ASN][1000 genomes]
rs500349	0.89[ASN][1000 genomes]
rs519319	0.89[ASN][1000 genomes]
rs539544	0.89[ASN][1000 genomes]
rs546445	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs548751	0.89[ASN][1000 genomes]
rs550892	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs566843	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs580828	0.89[ASN][1000 genomes]
rs6670960	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6696026	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703169	0.89[ASN][1000 genomes]
rs7555395	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6702666	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs6702666	RP4-717I23.3	cis	lung	GTEx
rs6702666	RP4-717I23.3	cis	Artery Aorta	GTEx
rs6702666	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6702666	RP4-717I23.3	cis	Thyroid	GTEx
rs6702666	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs6702666	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs6702666	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs6702666	RP4-717I23.3	cis	Whole Blood	GTEx
rs6702666	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs6702666	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs6702666	CCDC18	Cis_1M	lymphoblastoid	RTeQTL
rs6702666	RP4-717I23.3	cis	Artery Tibial	GTEx
rs6702666	RP4-717I23.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
2	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
4	chr1:93578800-93613600	Weak transcription	Psoas Muscle	Psoas
5	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:93581200-93616800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:93582400-93620400	Weak transcription	Small Intestine	intestine
10	chr1:93582400-93642800	Weak transcription	Gastric	stomach
11	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:93583600-93613800	Weak transcription	Lung	lung
13	chr1:93583600-93623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
15	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
16	chr1:93586200-93623400	Weak transcription	Fetal Brain Male	brain
17	chr1:93586800-93621000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:93591200-93612600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:93591400-93616600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:93593000-93614200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:93594400-93611400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:93595400-93612400	Weak transcription	Fetal Heart	heart
23	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:93597400-93625400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
26	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
27	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:93602000-93614000	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:93602600-93611400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:93602600-93613000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:93602600-93613200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:93602600-93613600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:93602600-93613600	Weak transcription	Ovary	ovary
34	chr1:93602600-93613600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:93602600-93613600	Weak transcription	A549	lung
36	chr1:93602600-93613800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:93602600-93613800	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:93602600-93614400	Weak transcription	NHLF	lung
39	chr1:93602600-93620400	Weak transcription	Fetal Stomach	stomach
40	chr1:93602600-93620600	Weak transcription	Colonic Mucosa	Colon
41	chr1:93602600-93620600	Weak transcription	Fetal Intestine Small	intestine
42	chr1:93602600-93624200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:93602600-93628800	Weak transcription	Aorta	Aorta
44	chr1:93602600-93630200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:93602600-93630200	Weak transcription	Brain Anterior Caudate	brain
46	chr1:93602800-93613000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:93602800-93613600	Weak transcription	Thymus	Thymus
48	chr1:93603200-93611600	Weak transcription	NHDF-Ad	bronchial
49	chr1:93603200-93614800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:93603400-93613200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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