Variant report

Variant	rs38441
Chromosome Location	chr7:30562952-30562953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:30562005..30563537-chr7:30563682..30566502,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCT-1	chr7:30562759-30564151	NONHSAT119876

Variant related genes	Relation type
ENSG00000244480	Chromatin interaction
ENSG00000264520	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1986756	0.86[CHB][hapmap]
rs2529437	0.86[CHB][hapmap]
rs2709809	0.86[CHB][hapmap]
rs28679	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38406	0.83[ASN][1000 genomes]
rs38407	0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38408	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38409	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs38410	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38411	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38413	0.88[CEU][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38414	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38415	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs38416	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38417	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs38418	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38419	0.91[ASN][1000 genomes]
rs38420	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs38421	0.86[ASN][1000 genomes]
rs38422	0.91[ASN][1000 genomes]
rs38423	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38425	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38426	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38427	0.91[ASN][1000 genomes]
rs38428	0.81[ASN][1000 genomes]
rs38429	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38430	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs38432	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38433	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs38434	0.81[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs38437	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs38438	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38440	0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs38442	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38443	0.88[ASN][1000 genomes]
rs38444	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38445	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38446	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38447	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38448	0.97[ASN][1000 genomes]
rs38450	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38451	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38452	0.97[ASN][1000 genomes]
rs38453	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38454	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38455	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38456	0.96[ASN][1000 genomes]
rs38458	0.96[ASN][1000 genomes]
rs38460	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38461	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs38462	0.96[ASN][1000 genomes]
rs38463	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38464	0.96[ASN][1000 genomes]
rs38465	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38466	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38467	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38468	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38469	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38471	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38472	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38473	0.90[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs38474	0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs38478	0.90[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs38480	0.85[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38481	0.87[ASN][1000 genomes]
rs38482	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38483	0.86[ASN][1000 genomes]
rs38487	0.85[CHB][hapmap]
rs38495	0.86[CHB][hapmap]
rs39738	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40237	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4258	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4259	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4260	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs973002	0.81[CHB][hapmap]
rs975537	0.85[CHB][hapmap]

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	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
2	nsv966770	chr7:30562144-30590529	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs38441	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38441	AC005154.6	cis	Nerve Tibial	GTEx
rs38441	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38441	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38441	AC005154.6	cis	Whole Blood	GTEx
rs38441	AC005154.6	cis	Stomach	GTEx
rs38441	AC005154.6	cis	Artery Tibial	GTEx
rs38441	AC005154.6	cis	Artery Aorta	GTEx
rs38441	AC005154.8	cis	Whole Blood	GTEx
rs38441	AC005154.6	cis	lung	GTEx
rs38441	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38441	AC005154.6	cis	Muscle Skeletal	GTEx
rs38441	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38441	AC005154.6	cis	Thyroid	GTEx
rs38441	AC005154.6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30545000-30584600	Weak transcription	Aorta	Aorta
2	chr7:30545200-30587600	Weak transcription	HSMMtube	muscle
3	chr7:30545400-30576200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:30545400-30576600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:30545600-30586200	Weak transcription	Brain Anterior Caudate	brain
6	chr7:30554000-30577600	Weak transcription	Placenta	Placenta
7	chr7:30554400-30596400	Weak transcription	Fetal Brain Female	brain
8	chr7:30554600-30574600	Weak transcription	Primary T cells from cord blood	blood
9	chr7:30554800-30588600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:30555200-30590800	Weak transcription	Spleen	Spleen
11	chr7:30558200-30568400	Enhancers	Fetal Intestine Large	intestine
12	chr7:30559200-30576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:30559800-30576400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:30560400-30563000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:30560400-30564400	Enhancers	Duodenum Mucosa	Duodenum
16	chr7:30560400-30564800	Weak transcription	K562	blood
17	chr7:30560400-30590800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:30560600-30563800	Weak transcription	Stomach Mucosa	stomach
19	chr7:30560600-30577000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:30560600-30588200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:30560800-30586400	Weak transcription	Primary B cells from cord blood	blood
22	chr7:30560800-30587600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:30560800-30588400	Weak transcription	Brain Substantia Nigra	brain
24	chr7:30561000-30564000	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:30561000-30565600	Weak transcription	Colonic Mucosa	Colon
26	chr7:30561000-30584600	Weak transcription	Ovary	ovary
27	chr7:30561200-30576600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr7:30561200-30576800	Weak transcription	Fetal Stomach	stomach
29	chr7:30561200-30590400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr7:30561200-30590600	Weak transcription	Right Ventricle	heart
31	chr7:30561400-30563000	Strong transcription	Brain Hippocampus Middle	brain
32	chr7:30561400-30564000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:30561400-30565600	Weak transcription	Right Atrium	heart
34	chr7:30561400-30580000	Weak transcription	Esophagus	oesophagus
35	chr7:30561400-30585200	Weak transcription	Fetal Lung	lung
36	chr7:30561600-30586000	Weak transcription	Left Ventricle	heart
37	chr7:30561600-30586000	Weak transcription	Lung	lung
38	chr7:30561600-30586200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:30561600-30590600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:30561600-30606400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:30561800-30563000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr7:30561800-30570200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:30561800-30573200	Weak transcription	Adipose Nuclei	Adipose
44	chr7:30561800-30573400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr7:30561800-30585000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:30562200-30563000	Enhancers	Small Intestine	intestine
47	chr7:30562200-30573200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr7:30562400-30563800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr7:30562600-30563800	Weak transcription	HepG2	liver
50	chr7:30562600-30564000	Genic enhancers	Fetal Intestine Small	intestine

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