Variant report

Variant	rs12060630
Chromosome Location	chr1:78071485-78071486
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	chr1:78070290..78072373-chr1:78147292..78150145,3	K562	blood:
2	chr1:78065469..78069224-chr1:78069679..78073239,3	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11162379	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6694137	1.00[ASW][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938038	1.00[AMR][1000 genomes]
rs7511779	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7535908	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78033200-78072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:78042000-78074600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:78042200-78073800	Weak transcription	Fetal Brain Female	brain
4	chr1:78047600-78071600	Weak transcription	Thymus	Thymus
5	chr1:78047600-78072400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:78047600-78072600	Weak transcription	Fetal Kidney	kidney
7	chr1:78047600-78074600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:78047600-78074800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:78047600-78085600	Weak transcription	NHLF	lung
10	chr1:78047800-78074200	Weak transcription	Hela-S3	cervix
11	chr1:78047800-78074800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:78047800-78086200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:78047800-78090000	Weak transcription	NH-A	brain
14	chr1:78048000-78074600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:78048000-78077800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:78048000-78097400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:78049000-78072400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:78050000-78075000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:78054000-78074800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:78056600-78074000	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:78058000-78074800	Weak transcription	Brain Germinal Matrix	brain
22	chr1:78059000-78083200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:78061200-78072400	Weak transcription	GM12878-XiMat	blood
24	chr1:78062800-78074200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:78063200-78083000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:78063600-78072200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:78063600-78073800	Weak transcription	Liver	Liver
28	chr1:78063600-78074000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:78063600-78074400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:78063600-78074800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:78063600-78075000	Weak transcription	Dnd41	blood
32	chr1:78063600-78097600	Weak transcription	Fetal Brain Male	brain
33	chr1:78064000-78071800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:78064200-78072000	Weak transcription	Fetal Thymus	thymus
35	chr1:78064200-78075200	Weak transcription	HepG2	liver
36	chr1:78064400-78074400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:78064600-78074400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:78068000-78071800	Weak transcription	HSMM	muscle
39	chr1:78069000-78072200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:78069400-78071600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:78069400-78072400	Weak transcription	Primary T cells from cord blood	blood
42	chr1:78069600-78074000	Weak transcription	A549	lung
43	chr1:78069800-78072200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr1:78070000-78071600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:78070200-78071600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:78070200-78071800	Enhancers	Brain Substantia Nigra	brain
47	chr1:78070200-78072200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:78070400-78072000	Enhancers	Right Atrium	heart
49	chr1:78070400-78072000	Enhancers	K562	blood
50	chr1:78070600-78071600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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