Variant report

Variant	rs60505849
Chromosome Location	chr12:39835028-39835029
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:39707343..39709850-chr12:39833796..39835957,2	K562	blood:
2	chr12:39807290..39809220-chr12:39833749..39836763,3	K562	blood:
3	chr12:39815681..39818065-chr12:39831801..39835369,3	K562	blood:
4	chr12:39834094..39836682-chr12:39930769..39933635,3	K562	blood:
5	chr12:39708256..39710912-chr12:39833762..39835679,2	MCF-7	breast:
6	chr12:39743944..39745971-chr12:39833401..39836053,2	K562	blood:
7	chr12:39806434..39808790-chr12:39833185..39835249,2	K562	blood:
8	chr12:39759047..39762172-chr12:39834495..39838400,6	MCF-7	breast:
9	chr12:39723120..39728244-chr12:39834929..39837982,4	MCF-7	breast:
10	chr12:39801655..39803705-chr12:39833812..39835448,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11171568	1.00[AFR][1000 genomes]
rs11171691	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11171786	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11171797	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11171857	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11172082	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172105	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172109	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172168	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172175	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172204	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172263	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172347	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172359	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172373	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172471	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11172474	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11172502	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11172566	0.88[EUR][1000 genomes]
rs11172603	0.85[EUR][1000 genomes]
rs11543371	0.88[EUR][1000 genomes]
rs12227092	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12227642	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12228285	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12228664	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17127115	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17127119	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56154721	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs58648215	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs59380486	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61453715	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788260	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39821400-39835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:39825200-39835600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:39829600-39835800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:39830000-39835400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:39832200-39835600	Enhancers	Liver	Liver
6	chr12:39833000-39835200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:39833600-39836400	Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr12:39833800-39835200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:39833800-39835600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:39833800-39836200	Active TSS	Brain Germinal Matrix	brain
11	chr12:39833800-39837800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:39834000-39835400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:39834000-39835400	Flanking Active TSS	A549	lung
14	chr12:39834000-39835400	Flanking Active TSS	K562	blood
15	chr12:39834000-39835600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:39834000-39837600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr12:39834000-39838000	Active TSS	Right Atrium	heart
18	chr12:39834200-39835200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:39834200-39835400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:39834200-39838000	Active TSS	Brain Angular Gyrus	brain
21	chr12:39834400-39835200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:39834400-39835200	Enhancers	Brain Hippocampus Middle	brain
23	chr12:39834400-39835400	Flanking Active TSS	HepG2	liver
24	chr12:39834400-39837400	Active TSS	Fetal Brain Female	brain
25	chr12:39834400-39837800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:39834400-39837800	Active TSS	Right Ventricle	heart
27	chr12:39834600-39835400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr12:39834600-39835400	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr12:39834600-39835400	Flanking Active TSS	Hela-S3	cervix
30	chr12:39834600-39835600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:39834600-39835600	Enhancers	Fetal Intestine Large	intestine
32	chr12:39834600-39835600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr12:39834800-39835200	Enhancers	Adipose Nuclei	Adipose
34	chr12:39834800-39835200	Enhancers	Fetal Intestine Small	intestine
35	chr12:39834800-39835400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:39834800-39835400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:39834800-39835400	Flanking Active TSS	Fetal Heart	heart
38	chr12:39834800-39835600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr12:39834800-39835600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:39834800-39835600	Weak transcription	Psoas Muscle	Psoas
41	chr12:39834800-39835600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr12:39834800-39835800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:39834800-39835800	Weak transcription	Pancreas	Pancrea
44	chr12:39834800-39836000	Weak transcription	Lung	lung
45	chr12:39834800-39837400	Active TSS	GM12878-XiMat	blood
46	chr12:39834800-39837600	Active TSS	Left Ventricle	heart
47	chr12:39835000-39835200	Active TSS	H1 Cell Line	embryonic stem cell
48	chr12:39835000-39835200	Active TSS	Brain Anterior Caudate	brain
49	chr12:39835000-39835200	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr12:39835000-39835200	Active TSS	Fetal Brain Male	brain

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