Variant report

Variant	rs3845634
Chromosome Location	chr2:211368358-211368359
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10184506	0.87[CEU][hapmap]
rs10195425	0.87[CEU][hapmap]
rs10932336	0.90[ASN][1000 genomes]
rs10932340	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12694200	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13005638	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13013076	0.82[JPT][hapmap]
rs1509816	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1858194	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1858195	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2160851	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287426	0.87[CEU][hapmap]
rs2287427	0.87[CEU][hapmap]
rs2370962	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2664239	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35003355	0.81[AMR][1000 genomes]
rs3732058	0.87[CEU][hapmap]
rs3755186	1.00[CEU][hapmap]
rs3755187	0.87[CEU][hapmap]
rs3770688	0.87[CEU][hapmap]
rs3770693	0.87[CEU][hapmap]
rs3770696	0.87[CEU][hapmap]
rs4672580	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672581	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672582	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57718949	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62203712	0.88[ASN][1000 genomes]
rs6749711	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6752530	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7590759	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs759688	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs759689	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs918234	0.87[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs9941507	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3459962	chr2:211360526-211368951	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3459963	chr2:211360858-211368614	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3845634	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211364200-211370200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:211364600-211368800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:211367400-211369000	Enhancers	Hela-S3	cervix
4	chr2:211367600-211368600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr2:211367600-211368600	Enhancers	HepG2	liver
6	chr2:211367600-211368800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:211367800-211368400	Active TSS	Colon Smooth Muscle	Colon
8	chr2:211367800-211368400	Active TSS	Fetal Muscle Leg	muscle
9	chr2:211367800-211368600	Enhancers	Primary hematopoietic stem cells	blood
10	chr2:211367800-211368600	Active TSS	Psoas Muscle	Psoas
11	chr2:211367800-211368600	Active TSS	A549	lung
12	chr2:211367800-211368800	Flanking Active TSS	Liver	Liver
13	chr2:211367800-211368800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr2:211367800-211368800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:211367800-211368800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr2:211368000-211368400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:211368000-211368400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:211368000-211368400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:211368000-211368400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:211368000-211368400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:211368000-211368400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:211368000-211368400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr2:211368000-211368400	Active TSS	Brain Hippocampus Middle	brain
24	chr2:211368000-211368400	Active TSS	Brain Substantia Nigra	brain
25	chr2:211368000-211368400	Active TSS	Stomach Mucosa	stomach
26	chr2:211368000-211368600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:211368000-211368600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:211368000-211368600	Active TSS	Ovary	ovary
29	chr2:211368000-211368600	Active TSS	HSMMtube	muscle
30	chr2:211368000-211368800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:211368000-211368800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr2:211368000-211368800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr2:211368000-211368800	Active TSS	Brain Angular Gyrus	brain
34	chr2:211368000-211368800	Active TSS	Brain Anterior Caudate	brain
35	chr2:211368000-211368800	Enhancers	Fetal Stomach	stomach
36	chr2:211368000-211368800	Active TSS	Stomach Smooth Muscle	stomach
37	chr2:211368000-211369000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:211368000-211369000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:211368000-211369000	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr2:211368000-211369000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr2:211368000-211369000	Active TSS	Fetal Muscle Trunk	muscle
42	chr2:211368000-211369200	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr2:211368200-211368400	Active TSS	Duodenum Mucosa	Duodenum
44	chr2:211368200-211368400	Enhancers	Fetal Kidney	kidney
45	chr2:211368200-211368400	Weak transcription	Pancreas	Pancrea
46	chr2:211368200-211368400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr2:211368200-211368400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:211368200-211368400	Flanking Active TSS	HSMM	muscle
49	chr2:211368200-211368600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:211368200-211368600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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