Variant report

Variant	rs3098377
Chromosome Location	chr5:5437016-5437017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:5421451..5422973-chr5:5435483..5438467,2	K562	blood:
2	chr5:5435223..5438170-chr5:5438538..5441518,2	K562	blood:

Variant related genes	Relation type
ENSG00000164151	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10063885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12653733	0.80[CEU][hapmap]
rs1541799	0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2560297	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560298	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2560299	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560300	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578500	0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs2578548	0.80[EUR][1000 genomes]
rs2578549	0.85[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578550	0.81[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2578552	0.89[ASW][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2578553	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578556	0.87[EUR][1000 genomes]
rs2578557	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2578558	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2578564	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578565	0.87[TSI][hapmap]
rs2619827	0.83[EUR][1000 genomes]
rs2619844	0.85[EUR][1000 genomes]
rs2918253	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2918260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918261	0.90[TSI][hapmap]
rs2964131	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964160	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3097160	0.81[EUR][1000 genomes]
rs3111175	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61063822	0.83[EUR][1000 genomes]
rs6894118	0.85[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021802	chr5:5415877-5452886	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv528309	chr5:5434937-5452839	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3098377	NDUFS6	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5424400-5437200	Weak transcription	Fetal Thymus	thymus
2	chr5:5424400-5437400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:5424400-5437600	Weak transcription	Placenta	Placenta
4	chr5:5424800-5437600	Weak transcription	Fetal Kidney	kidney
5	chr5:5425000-5437200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:5425000-5437200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:5425000-5437600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:5425000-5437800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:5425000-5443600	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:5425200-5439000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:5425200-5443200	Weak transcription	Fetal Brain Male	brain
12	chr5:5425200-5443600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:5425200-5443600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:5425200-5443600	Weak transcription	Pancreas	Pancrea
15	chr5:5425200-5443800	Weak transcription	Esophagus	oesophagus
16	chr5:5425400-5441400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr5:5425400-5443600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:5425400-5443800	Weak transcription	Colonic Mucosa	Colon
19	chr5:5425600-5437200	Weak transcription	Fetal Lung	lung
20	chr5:5425600-5440800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:5425600-5443400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr5:5425600-5443400	Weak transcription	Brain Germinal Matrix	brain
23	chr5:5425600-5443600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:5425600-5443600	Weak transcription	Thymus	Thymus
25	chr5:5425800-5443200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:5426000-5443200	Weak transcription	Brain Anterior Caudate	brain
27	chr5:5426200-5437200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:5428000-5444800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:5428400-5443600	Weak transcription	Right Ventricle	heart
30	chr5:5428600-5437200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:5428600-5437400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:5429200-5437600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:5429600-5443400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:5430000-5437800	Weak transcription	Fetal Stomach	stomach
35	chr5:5430200-5437600	Weak transcription	A549	lung
36	chr5:5430200-5478800	Weak transcription	Stomach Mucosa	stomach
37	chr5:5430400-5443600	Weak transcription	Gastric	stomach
38	chr5:5430400-5443600	Weak transcription	Lung	lung
39	chr5:5430800-5460800	Weak transcription	Fetal Heart	heart
40	chr5:5431200-5437400	Weak transcription	HepG2	liver
41	chr5:5431200-5437400	Weak transcription	NHLF	lung
42	chr5:5431600-5437600	Weak transcription	Left Ventricle	heart
43	chr5:5431800-5442200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:5432000-5441200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:5432400-5437800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr5:5432600-5437200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:5432600-5437400	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:5432600-5437400	Weak transcription	NHDF-Ad	bronchial
49	chr5:5432600-5443200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:5432800-5437200	Weak transcription	NH-A	brain

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