Variant report

Variant	rs16987411
Chromosome Location	chr2:20349026-20349027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20344027..20347003-chr2:20348055..20350773,2	MCF-7	breast:
2	chr2:20165489..20167886-chr2:20346989..20349091,2	K562	blood:
3	chr2:20348708..20350605-chr2:20350801..20352836,2	MCF-7	breast:
4	chr2:20343488..20346809-chr2:20347899..20350701,3	MCF-7	breast:
5	chr2:20348330..20350992-chr2:20378144..20381464,4	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1107850	0.92[JPT][hapmap]
rs11096642	0.86[JPT][hapmap]
rs11673796	0.86[JPT][hapmap]
rs11678701	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685359	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692531	0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13019898	0.84[GIH][hapmap]
rs59186438	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61252483	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62112223	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1005923	chr2:20344028-20369781	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv581156	chr2:20346312-20356944	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16987411	LAMC1	trans	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20339600-20349200	Weak transcription	Small Intestine	intestine
3	chr2:20345600-20349800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:20345600-20356600	Weak transcription	Liver	Liver
5	chr2:20345800-20349200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:20345800-20349200	Weak transcription	Gastric	stomach
7	chr2:20346000-20349400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:20346000-20355600	Weak transcription	Esophagus	oesophagus
9	chr2:20346400-20349200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:20346800-20352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:20348000-20349400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:20348000-20349600	Enhancers	Brain Germinal Matrix	brain
13	chr2:20348000-20349800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr2:20348000-20349800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:20348000-20351200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:20348000-20351400	Enhancers	HSMM	muscle
17	chr2:20348200-20349400	Weak transcription	Lung	lung
18	chr2:20348200-20349600	Enhancers	Fetal Kidney	kidney
19	chr2:20348200-20349800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:20348200-20350000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:20348200-20351200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr2:20348400-20349200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:20348400-20349200	Enhancers	Brain Substantia Nigra	brain
24	chr2:20348400-20349400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:20348400-20349600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:20348400-20349600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:20348400-20349600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:20348400-20349600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:20348400-20349600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:20348400-20349600	Enhancers	K562	blood
31	chr2:20348400-20349600	Flanking Active TSS	NH-A	brain
32	chr2:20348400-20349800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:20348400-20349800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr2:20348400-20350000	Enhancers	HMEC	breast
35	chr2:20348400-20350000	Enhancers	NHLF	lung
36	chr2:20348400-20350400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr2:20348400-20351200	Enhancers	Fetal Lung	lung
38	chr2:20348400-20351400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:20348600-20349200	Flanking Active TSS	Stomach Mucosa	stomach
40	chr2:20348600-20349200	Flanking Active TSS	HepG2	liver
41	chr2:20348600-20349400	Enhancers	Fetal Intestine Small	intestine
42	chr2:20348600-20349600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr2:20348600-20349600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr2:20348600-20349600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:20348600-20349600	Enhancers	Adipose Nuclei	Adipose
46	chr2:20348600-20349600	Enhancers	A549	lung
47	chr2:20348600-20349600	Enhancers	Hela-S3	cervix
48	chr2:20348600-20349800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:20348600-20349800	Enhancers	Duodenum Mucosa	Duodenum
50	chr2:20348600-20349800	Enhancers	Placenta	Placenta

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