Variant report

Variant	rs3741635
Chromosome Location	chr12:106136330-106136331
allele	C/T
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:1)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106134598..106137615-chr12:106531407..106534871,3	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf75-2	chr12:106135534-106137840	ENSG00000257859
2	lnc-C12orf75-2	chr12:106135534-106137841	NR_110108
3	lnc-C12orf75-2	chr12:106135534-106137841	NR_110109
4	lnc-C12orf75-2	chr12:106135534-106137841	NR_110110
5	lnc-C12orf75-2	chr12:106135534-106137841	NR_110111

No data

Variant related genes	Relation type
ENSG00000074590	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10861495	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11834526	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374545	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61940062	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137045	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307913	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv1039068	chr12:105935786-106211250	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899503	chr12:106021477-106175903	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1047810	chr12:106067049-106246582	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1040261	chr12:106068992-106246582	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3447181	chr12:106132354-106138639	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3741635	BTBD11	cis	parietal	SCAN
rs3741635	NUAK1	cis	cerebellum	SCAN
rs3741635	TDG	cis	parietal	SCAN
rs3741635	NR1H4	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106130000-106137800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:106131800-106136600	Enhancers	Right Atrium	heart
3	chr12:106131800-106138000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:106132200-106137800	Enhancers	Fetal Muscle Leg	muscle
5	chr12:106132600-106136800	Enhancers	Brain Angular Gyrus	brain
6	chr12:106132800-106136600	Enhancers	Psoas Muscle	Psoas
7	chr12:106133600-106136600	Enhancers	Brain Germinal Matrix	brain
8	chr12:106133800-106137000	Enhancers	Fetal Stomach	stomach
9	chr12:106134000-106136400	Enhancers	Brain Cingulate Gyrus	brain
10	chr12:106134000-106136400	Enhancers	Fetal Heart	heart
11	chr12:106134000-106136600	Enhancers	Brain Hippocampus Middle	brain
12	chr12:106134200-106136400	Enhancers	HSMM	muscle
13	chr12:106134200-106136400	Enhancers	NHDF-Ad	bronchial
14	chr12:106134200-106136600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:106134200-106136600	Enhancers	Adipose Nuclei	Adipose
16	chr12:106134200-106136600	Enhancers	Aorta	Aorta
17	chr12:106134200-106136600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr12:106134200-106136600	Enhancers	Ovary	ovary
19	chr12:106134200-106136600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr12:106134200-106136800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:106134200-106137000	Enhancers	Left Ventricle	heart
22	chr12:106134400-106136600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:106134600-106136400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:106134600-106136400	Enhancers	NH-A	brain
25	chr12:106134600-106136600	Enhancers	Fetal Lung	lung
26	chr12:106134800-106136400	Enhancers	Brain Substantia Nigra	brain
27	chr12:106134800-106136400	Enhancers	Osteobl	bone
28	chr12:106134800-106136600	Enhancers	Placenta	Placenta
29	chr12:106134800-106136800	Enhancers	Right Ventricle	heart
30	chr12:106134800-106137200	Enhancers	Fetal Brain Female	brain
31	chr12:106135000-106137400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:106135200-106136400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:106135200-106137600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:106135400-106136400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:106135400-106137400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:106135400-106138200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:106135400-106138200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:106135400-106139000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:106135400-106142400	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:106135600-106136800	Enhancers	Duodenum Mucosa	Duodenum
41	chr12:106135600-106137000	Genic enhancers	HSMMtube	muscle
42	chr12:106135600-106137200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:106135800-106136600	Enhancers	Stomach Smooth Muscle	stomach
44	chr12:106135800-106137600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:106135800-106137600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:106135800-106138400	Enhancers	Fetal Brain Male	brain
47	chr12:106135800-106139000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:106136000-106136600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:106136000-106136600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:106136000-106136600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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