Variant report

Variant	rs11895784
Chromosome Location	chr2:211294890-211294891
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:211293517..211296433-chr2:211339377..211342364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115365	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1009906	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1027902	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10932331	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10932332	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11884252	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12465418	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12474078	0.81[CEU][hapmap]
rs1458281	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1458288	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16844516	0.91[JPT][hapmap]
rs17769570	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17770211	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17820639	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2042049	0.81[CEU][hapmap]
rs2370952	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2370954	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3732055	0.82[CEU][hapmap]
rs3856338	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3900166	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4102442	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55789407	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56063685	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56398195	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7425115	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7602073	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7602360	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs988726	0.94[AFR][1000 genomes];0.89[AMR][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	nsv1012567	chr2:211087588-211315554	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv3147	chr2:211281479-211326844	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11895784	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211287200-211298200	Weak transcription	HMEC	breast
2	chr2:211287200-211299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:211287200-211299600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:211287400-211296000	Weak transcription	HSMM	muscle
5	chr2:211287400-211297800	Weak transcription	NH-A	brain
6	chr2:211287800-211295600	Weak transcription	Brain Anterior Caudate	brain
7	chr2:211288400-211296600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:211290600-211299000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:211291400-211297200	Weak transcription	Ovary	ovary
10	chr2:211291400-211299400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:211291600-211295200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:211291600-211295800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:211291600-211296000	Weak transcription	NHDF-Ad	bronchial
14	chr2:211291600-211296400	Weak transcription	Osteobl	bone
15	chr2:211291600-211299000	Weak transcription	Lung	lung
16	chr2:211291600-211300800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:211291800-211299600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:211292200-211295600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:211292200-211296000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr2:211292200-211297400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:211292200-211297400	Weak transcription	Thymus	Thymus
22	chr2:211292400-211295800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:211292400-211296200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:211292400-211323000	Weak transcription	Fetal Brain Male	brain
25	chr2:211292600-211295000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:211292600-211295600	Weak transcription	Fetal Stomach	stomach
27	chr2:211292600-211295800	Weak transcription	Fetal Brain Female	brain
28	chr2:211292800-211295200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:211293000-211295800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:211293000-211295800	Weak transcription	Liver	Liver
31	chr2:211293000-211295800	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:211293000-211296000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:211293000-211299400	Weak transcription	Esophagus	oesophagus
34	chr2:211293000-211305800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:211293200-211295600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:211293200-211295600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:211293200-211295800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:211293200-211295800	Weak transcription	Fetal Thymus	thymus
39	chr2:211293200-211296000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:211293200-211296000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:211293200-211296000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:211293200-211296000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:211293200-211296000	Weak transcription	Fetal Intestine Large	intestine
44	chr2:211293200-211297000	Weak transcription	Psoas Muscle	Psoas
45	chr2:211293200-211297200	Weak transcription	Aorta	Aorta
46	chr2:211293200-211297200	Weak transcription	Left Ventricle	heart
47	chr2:211293200-211297800	Weak transcription	Fetal Kidney	kidney
48	chr2:211293200-211299000	Weak transcription	Brain Germinal Matrix	brain
49	chr2:211293200-211299000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:211293200-211299200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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