Variant report

Variant	rs2296744
Chromosome Location	chr6:33740382-33740383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33731707..33733377-chr6:33739681..33741307,2	K562	blood:
2	chr6:33733922..33735455-chr6:33738926..33740913,2	MCF-7	breast:
3	chr6:33736395..33737905-chr6:33740079..33742724,2	K562	blood:
4	chr6:33677151..33680603-chr6:33737180..33740397,3	MCF-7	breast:
5	chr6:33738171..33740892-chr6:33996773..33998948,2	K562	blood:
6	chr6:33697484..33700204-chr6:33739217..33741356,2	MCF-7	breast:
7	chr6:33738877..33740467-chr6:33741508..33744175,2	K562	blood:
8	chr6:33717026..33719225-chr6:33737928..33740540,2	MCF-7	breast:
9	chr6:33737959..33740435-chr6:34032927..34035702,2	K562	blood:
10	chr6:33738726..33740587-chr6:33954183..33956519,2	MCF-7	breast:
11	chr6:33738877..33741098-chr6:33742637..33744175,2	K562	blood:
12	chr6:33558047..33560338-chr6:33737884..33740577,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12173787	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12190029	0.81[EUR][1000 genomes]
rs2281820	0.92[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2296743	0.81[ASW][hapmap];0.84[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs2395402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3793079	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs3806108	0.81[ASW][hapmap];0.92[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs3806109	0.81[ASW][hapmap]
rs3806110	0.81[ASW][hapmap]
rs4711347	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711348	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4711349	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4711351	0.88[AFR][1000 genomes]
rs4711355	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4713678	0.81[EUR][1000 genomes]
rs4713679	0.87[EUR][1000 genomes]
rs6457741	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6922275	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6929696	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs747694	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7774620	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9357164	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9394167	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9394168	0.88[AFR][1000 genomes]
rs943471	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs943474	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs943475	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs943477	0.88[AFR][1000 genomes]
rs943478	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs943479	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2296744	LEMD2	cis	parietal	SCAN
rs2296744	LEMD2	cis	cerebellum	SCAN
rs2296744	PSMB9	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33732600-33742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:33736200-33740600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr6:33736800-33741000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:33736800-33743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:33737600-33740600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:33737800-33740400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:33737800-33742600	Weak transcription	Hela-S3	cervix
8	chr6:33738000-33741000	Enhancers	NHDF-Ad	bronchial
9	chr6:33738200-33740400	Enhancers	Stomach Mucosa	stomach
10	chr6:33738600-33740600	Genic enhancers	Fetal Intestine Small	intestine
11	chr6:33738600-33741400	Genic enhancers	Fetal Stomach	stomach
12	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
13	chr6:33738800-33740400	Weak transcription	Small Intestine	intestine
14	chr6:33738800-33740600	Genic enhancers	A549	lung
15	chr6:33738800-33741800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:33738800-33741800	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr6:33739000-33740400	Weak transcription	Aorta	Aorta
18	chr6:33739000-33740600	Weak transcription	Fetal Kidney	kidney
19	chr6:33739000-33741400	Enhancers	Fetal Brain Male	brain
20	chr6:33739000-33741400	Enhancers	HSMM	muscle
21	chr6:33739000-33741600	Enhancers	HSMMtube	muscle
22	chr6:33739000-33746000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:33739200-33740400	Enhancers	K562	blood
24	chr6:33739600-33741400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:33739600-33742000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:33739800-33740400	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr6:33739800-33740400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:33739800-33740400	Genic enhancers	Colon Smooth Muscle	Colon
31	chr6:33739800-33740400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr6:33739800-33740600	Genic enhancers	Adipose Nuclei	Adipose
33	chr6:33739800-33740600	Genic enhancers	Fetal Intestine Large	intestine
34	chr6:33739800-33740600	Enhancers	Ovary	ovary
35	chr6:33739800-33740800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:33739800-33740800	Genic enhancers	Spleen	Spleen
37	chr6:33739800-33741000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:33739800-33741000	Genic enhancers	Fetal Thymus	thymus
39	chr6:33739800-33741000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr6:33739800-33741000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:33739800-33741400	Genic enhancers	Placenta	Placenta
42	chr6:33739800-33741600	Genic enhancers	Esophagus	oesophagus
43	chr6:33739800-33741600	Genic enhancers	Fetal Muscle Leg	muscle
44	chr6:33739800-33741800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:33739800-33741800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:33739800-33741800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:33739800-33741800	Genic enhancers	Brain Hippocampus Middle	brain
48	chr6:33739800-33741800	Genic enhancers	NHLF	lung
49	chr6:33739800-33742000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:33739800-33742000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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