Variant report

Variant	rs38434
Chromosome Location	chr7:30554997-30554998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:30553250..30555674-chr7:30559176..30561267,2	MCF-7	breast:
2	chr7:30554141..30556628-chr7:30633622..30636219,2	K562	blood:
3	chr7:30554900..30557427-chr7:30557872..30559739,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GARS-8	chr7:30554988-30555585	NONHSAT119871
2	lnc-GGCT-1	chr7:30554500-30556922	ucscGeneNc_uc003tbf_1

Variant related genes	Relation type
ENSG00000196295	Chromatin interaction
ENSG00000106105	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs28679	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38406	0.88[ASN][1000 genomes]
rs38407	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs38408	0.91[ASN][1000 genomes]
rs38409	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38410	0.91[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38411	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38413	0.81[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38414	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38415	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs38416	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38417	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38418	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38419	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38420	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38421	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38422	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38423	0.99[ASN][1000 genomes]
rs38425	0.99[ASN][1000 genomes]
rs38426	0.99[ASN][1000 genomes]
rs38427	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38428	0.88[ASN][1000 genomes]
rs38429	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38432	0.99[ASN][1000 genomes]
rs38433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38435	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38436	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38437	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38438	0.97[ASN][1000 genomes]
rs38440	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38441	0.81[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs38442	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs38443	0.83[ASN][1000 genomes]
rs38444	0.88[ASN][1000 genomes]
rs38445	0.89[ASN][1000 genomes]
rs38446	0.89[ASN][1000 genomes]
rs38447	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38448	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38450	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38451	0.88[ASN][1000 genomes]
rs38452	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38453	0.88[ASN][1000 genomes]
rs38454	0.88[ASN][1000 genomes]
rs38455	0.86[ASN][1000 genomes]
rs38456	0.89[ASN][1000 genomes]
rs38458	0.89[ASN][1000 genomes]
rs38460	0.88[ASN][1000 genomes]
rs38461	0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs38462	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38463	0.88[ASN][1000 genomes]
rs38464	0.89[ASN][1000 genomes]
rs38465	0.87[ASN][1000 genomes]
rs38466	0.83[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs38467	0.83[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs38468	0.83[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs38469	0.83[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs38471	0.83[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs38472	0.84[ASN][1000 genomes]
rs38473	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38474	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs38478	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38480	0.82[ASN][1000 genomes]
rs38481	0.83[ASN][1000 genomes]
rs38483	0.83[ASN][1000 genomes]
rs38488	0.83[TSI][hapmap]
rs39738	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs40237	0.99[ASN][1000 genomes]
rs4258	0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4259	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4260	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs973002	1.00[ASW][hapmap];0.83[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs38434	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38434	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38434	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38434	AC005154.6	cis	Artery Tibial	GTEx
rs38434	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38434	AC005154.6	cis	Stomach	GTEx
rs38434	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38434	AC005154.6	cis	Nerve Tibial	GTEx
rs38434	AC005154.6	cis	lung	GTEx
rs38434	AC005154.6	cis	Muscle Skeletal	GTEx
rs38434	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38434	AC005154.8	cis	Whole Blood	GTEx
rs38434	AC005154.6	cis	Thyroid	GTEx
rs38434	AC005154.6	cis	Artery Aorta	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30545000-30584600	Weak transcription	Aorta	Aorta
2	chr7:30545200-30556800	Weak transcription	Pancreas	Pancrea
3	chr7:30545200-30559800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr7:30545200-30562200	Weak transcription	Small Intestine	intestine
5	chr7:30545200-30587600	Weak transcription	HSMMtube	muscle
6	chr7:30545400-30559600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr7:30545400-30560200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:30545400-30560600	Weak transcription	Brain Substantia Nigra	brain
9	chr7:30545400-30560600	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:30545400-30576200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:30545400-30576600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:30545600-30586200	Weak transcription	Brain Anterior Caudate	brain
13	chr7:30550600-30559600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:30550600-30559600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr7:30551400-30555600	Weak transcription	Lung	lung
16	chr7:30552200-30559800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:30553000-30556400	Weak transcription	Fetal Intestine Small	intestine
18	chr7:30553200-30558200	Weak transcription	Fetal Intestine Large	intestine
19	chr7:30554000-30577600	Weak transcription	Placenta	Placenta
20	chr7:30554200-30560400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr7:30554200-30561400	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:30554400-30555200	Weak transcription	Fetal Brain Male	brain
23	chr7:30554400-30596400	Weak transcription	Fetal Brain Female	brain
24	chr7:30554600-30574600	Weak transcription	Primary T cells from cord blood	blood
25	chr7:30554800-30588600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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