Variant report

Variant	rs6877893
Chromosome Location	chr5:142727193-142727194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:142726115..142728667-chr5:142731602..142734053,2	MCF-7	breast:
2	chr5:142719538..142722482-chr5:142727185..142728885,2	K562	blood:
3	chr5:142726451..142729258-chr5:142734452..142735990,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10041520	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10482682	0.91[GIH][hapmap]
rs258747	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs258763	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33383	0.94[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33388	0.88[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4634384	0.90[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6191	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7716360	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs852976	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs852980	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs852983	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853180	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs853183	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[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	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1033408	chr5:142701353-142738882	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6877893	NR3C1	Cis_1M	lymphoblastoid	RTeQTL
rs6877893	LARS	cis	cerebellum	SCAN
rs6877893	PCDHB16	cis	cerebellum	SCAN
rs6877893	NR3C1	cis	parietal	SCAN
rs6877893	PCDHB9	cis	cerebellum	SCAN
rs6877893	SRA1	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142693800-142747400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:142703000-142727200	Weak transcription	HSMM	muscle
3	chr5:142704200-142728800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:142707400-142734800	Weak transcription	Placenta	Placenta
5	chr5:142707800-142727400	Weak transcription	Fetal Muscle Leg	muscle
6	chr5:142708000-142727200	Weak transcription	Fetal Thymus	thymus
7	chr5:142708000-142727400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr5:142708000-142728800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:142708000-142735400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:142708000-142735400	Weak transcription	Fetal Stomach	stomach
11	chr5:142711800-142728600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:142716000-142730200	Weak transcription	Fetal Lung	lung
13	chr5:142716600-142734200	Weak transcription	Ovary	ovary
14	chr5:142719400-142735400	Weak transcription	Gastric	stomach
15	chr5:142721200-142727800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:142722200-142728600	Weak transcription	HMEC	breast
17	chr5:142722400-142727200	Weak transcription	Hela-S3	cervix
18	chr5:142722400-142728800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:142722400-142728800	Weak transcription	NHEK	skin
20	chr5:142722800-142735400	Weak transcription	Pancreas	Pancrea
21	chr5:142723000-142727200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:142723000-142727200	Weak transcription	NHLF	lung
23	chr5:142723000-142727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:142723000-142727400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:142723000-142727400	Weak transcription	Left Ventricle	heart
26	chr5:142723000-142727400	Weak transcription	Psoas Muscle	Psoas
27	chr5:142723000-142727400	Weak transcription	Right Atrium	heart
28	chr5:142723000-142727400	Weak transcription	Thymus	Thymus
29	chr5:142723400-142728600	Weak transcription	K562	blood
30	chr5:142723400-142729000	Weak transcription	Small Intestine	intestine
31	chr5:142724400-142738000	Enhancers	Liver	Liver
32	chr5:142725000-142727200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:142725000-142731000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr5:142725000-142764200	Weak transcription	Lung	lung
35	chr5:142725200-142732400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:142725200-142737000	Weak transcription	Fetal Intestine Small	intestine
37	chr5:142725400-142727400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:142725400-142728200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:142725400-142731000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr5:142725400-142733400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr5:142725400-142735200	Enhancers	Brain Hippocampus Middle	brain
42	chr5:142725400-142737200	Enhancers	Brain Cingulate Gyrus	brain
43	chr5:142725600-142727600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:142725600-142728200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:142725600-142728400	Enhancers	Brain Substantia Nigra	brain
46	chr5:142725600-142728400	Genic enhancers	A549	lung
47	chr5:142725600-142730200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:142725600-142731600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr5:142725600-142731800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr5:142725600-142731800	Enhancers	Skeletal Muscle Male	skeletal muscle

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