Variant report

Variant	rs10877895
Chromosome Location	chr12:63023970-63023971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62996090..62998530-chr12:63021670..63024116,3	MCF-7	breast:
2	chr12:63017661..63021132-chr12:63021138..63024799,3	K562	blood:
3	chr12:63013376..63014961-chr12:63023890..63026114,2	K562	blood:
4	chr12:63023335..63025225-chr12:63026338..63028730,2	K562	blood:

Variant related genes	Relation type
ENSG00000199179	Chromatin interaction
ENSG00000221949	Chromatin interaction
ENSG00000257354	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10160870	0.88[ASN][1000 genomes]
rs10506444	0.82[JPT][hapmap]
rs10735910	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10747968	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784312	0.87[ASN][1000 genomes]
rs10877889	0.81[CHB][hapmap]
rs10877890	0.86[ASN][1000 genomes]
rs10877893	0.81[ASN][1000 genomes]
rs10877896	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs10877897	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877898	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877899	0.94[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11174573	0.81[CHB][hapmap]
rs11174574	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12582199	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498712	0.81[CHB][hapmap]
rs1498716	0.82[JPT][hapmap]
rs2133303	0.81[ASN][1000 genomes]
rs2359381	0.81[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs4763184	0.91[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs4763187	0.82[JPT][hapmap]
rs4763188	0.82[JPT][hapmap]
rs4763189	0.82[JPT][hapmap]
rs7308938	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7968360	0.81[CHB][hapmap]
rs907486	0.88[ASN][1000 genomes]
rs907487	0.88[ASN][1000 genomes]
rs925461	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs964644	0.82[JPT][hapmap]
rs9971786	0.82[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10877895	GLI1	cis	parietal	SCAN
rs10877895	AGAP2	cis	parietal	SCAN
rs10877895	CTDSP2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62999400-63025000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:63000800-63024200	Weak transcription	Fetal Brain Female	brain
3	chr12:63007800-63024800	Weak transcription	NH-A	brain
4	chr12:63010200-63025200	Weak transcription	HSMMtube	muscle
5	chr12:63013800-63025200	Weak transcription	Right Atrium	heart
6	chr12:63019400-63025000	Weak transcription	Adipose Nuclei	Adipose
7	chr12:63019600-63025400	Weak transcription	Pancreas	Pancrea
8	chr12:63019800-63025200	Weak transcription	Liver	Liver
9	chr12:63019800-63025800	Weak transcription	Placenta	Placenta
10	chr12:63021200-63024000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:63021400-63025200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:63021800-63024000	Weak transcription	HMEC	breast
13	chr12:63022200-63025600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:63022400-63024200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:63022400-63024200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:63022400-63024600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr12:63022600-63024600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:63022600-63025400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:63022600-63027000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:63022800-63024200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr12:63022800-63024400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:63022800-63024600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:63023000-63025000	Enhancers	Osteobl	bone
24	chr12:63023200-63024000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:63023200-63024000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:63023200-63024400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:63023200-63024800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:63023400-63025000	Enhancers	A549	lung
29	chr12:63023600-63024400	Weak transcription	Fetal Brain Male	brain
30	chr12:63023600-63025000	Enhancers	NHDF-Ad	bronchial
31	chr12:63023600-63025400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:63023800-63024000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr12:63023800-63024000	Enhancers	Fetal Kidney	kidney
34	chr12:63023800-63024200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr12:63023800-63024200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr12:63023800-63024200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
37	chr12:63023800-63024200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:63023800-63024400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:63023800-63024800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr12:63023800-63025000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
41	chr12:63023800-63025400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
42	chr12:63023800-63025400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
43	chr12:63023800-63025400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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