Variant report

Variant	rs12203115
Chromosome Location	chr6:36490733-36490734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36490465..36493524-chr6:36513455..36516315,3	MCF-7	breast:
2	chr6:36488938..36493688-chr6:36561807..36564126,6	MCF-7	breast:
3	chr6:36490205..36492952-chr6:36495728..36497599,2	MCF-7	breast:
4	chr6:36487455..36494660-chr6:36559051..36563997,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112081	Chromatin interaction
ENSG00000112079	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12208229	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3176327	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv5260	chr6:36471464-36516119	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12203115	LEMD2	cis	cerebellum	SCAN
rs12203115	FANCD2	trans	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36456400-36512600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:36463000-36507200	Weak transcription	Fetal Brain Male	brain
3	chr6:36463600-36493600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr6:36463800-36493400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr6:36463800-36513600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:36470600-36498800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:36473600-36491400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:36473600-36492200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:36473600-36500000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:36474000-36495200	Weak transcription	Fetal Heart	heart
11	chr6:36476200-36497800	Strong transcription	Dnd41	blood
12	chr6:36476800-36512200	Weak transcription	Brain Angular Gyrus	brain
13	chr6:36477400-36507400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr6:36478400-36493600	Weak transcription	Esophagus	oesophagus
15	chr6:36478400-36507400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:36478400-36507800	Strong transcription	Fetal Thymus	thymus
17	chr6:36478400-36513600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:36478400-36514000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:36478600-36493000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:36478800-36497400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:36478800-36512400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:36479000-36493000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:36479200-36491400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:36479600-36514400	Weak transcription	Spleen	Spleen
25	chr6:36480200-36493800	Weak transcription	Stomach Mucosa	stomach
26	chr6:36480200-36496000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:36481400-36512000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:36481800-36493800	Strong transcription	HSMMtube	muscle
29	chr6:36482000-36493600	Strong transcription	Adipose Nuclei	Adipose
30	chr6:36482000-36493800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:36482000-36494000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:36482200-36493400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:36482200-36494200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:36482600-36491400	Strong transcription	Osteobl	bone
35	chr6:36482600-36493400	Strong transcription	Primary B cells from cord blood	blood
36	chr6:36483200-36491400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:36483200-36500000	Weak transcription	Lung	lung
38	chr6:36483600-36493600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:36484000-36491400	Weak transcription	NHLF	lung
40	chr6:36484000-36491800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:36484000-36492600	Weak transcription	NHEK	skin
42	chr6:36484200-36493200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:36484200-36493400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:36484200-36506200	Weak transcription	Brain Substantia Nigra	brain
45	chr6:36484400-36492000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:36484600-36493600	Strong transcription	Placenta	Placenta
47	chr6:36484600-36493600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr6:36484600-36507600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:36484600-36514000	Weak transcription	Pancreas	Pancrea
50	chr6:36484800-36491400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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