Variant report

Variant	rs12055625
Chromosome Location	chr6:28094432-28094433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28092672..28095102-chr6:28302623..28304601,2	MCF-7	breast:
2	chr6:28091137..28098786-chr6:28103559..28111884,14	MCF-7	breast:
3	chr6:28069766..28072466-chr6:28092411..28094495,2	MCF-7	breast:
4	chr6:28089193..28090739-chr6:28092491..28094959,2	MCF-7	breast:
5	chr6:28089970..28093154-chr6:28093915..28098032,5	K562	blood:

Variant related genes	Relation type
ENSG00000261839	Chromatin interaction
ENSG00000196812	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1321504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321505	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13437126	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13437444	0.83[ASN][1000 genomes]
rs149943	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs149990	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs16893573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16893601	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16893735	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs202906	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs34130214	0.85[ASN][1000 genomes]
rs34712084	0.85[ASN][1000 genomes]
rs3734571	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3757188	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs4713138	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4713139	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs4713140	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs61127718	0.87[EUR][1000 genomes]
rs735765	0.90[CHD][hapmap]
rs8180562	0.82[ASN][1000 genomes]
rs904142	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9357064	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9368561	0.82[ASN][1000 genomes]
rs9380030	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9380031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9380032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9380045	1.00[CEU][hapmap]
rs9380051	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs9380064	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs9393882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9393889	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9393902	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9461432	0.85[ASN][1000 genomes]
rs9461439	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9468271	1.00[CEU][hapmap]
rs9468275	1.00[CEU][hapmap]
rs9468287	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs9468301	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12055625	HIST1H4J	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28082600-28096200	Strong transcription	Dnd41	blood
2	chr6:28091200-28096600	Strong transcription	K562	blood
3	chr6:28092800-28094600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:28092800-28094600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:28092800-28101800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:28092800-28103800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:28092800-28103800	Weak transcription	Ovary	ovary
8	chr6:28092800-28104000	Weak transcription	Aorta	Aorta
9	chr6:28092800-28104000	Weak transcription	Small Intestine	intestine
10	chr6:28092800-28104200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:28093000-28094600	Weak transcription	Fetal Kidney	kidney
12	chr6:28093000-28095000	Weak transcription	Osteobl	bone
13	chr6:28093000-28095200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:28093000-28096000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:28093000-28096200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:28093000-28096200	Weak transcription	HSMMtube	muscle
17	chr6:28093000-28096600	Weak transcription	NH-A	brain
18	chr6:28093000-28100200	Weak transcription	Brain Anterior Caudate	brain
19	chr6:28093000-28100800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:28093000-28103200	Weak transcription	NHLF	lung
21	chr6:28093000-28103800	Weak transcription	Psoas Muscle	Psoas
22	chr6:28093000-28104000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:28093000-28104200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:28093200-28094600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:28093200-28095000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:28093200-28095800	Weak transcription	Fetal Lung	lung
27	chr6:28093200-28096000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:28093200-28096200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:28093200-28097600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:28093200-28102400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:28093200-28103200	Weak transcription	HMEC	breast
32	chr6:28093200-28103600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:28093400-28094600	Weak transcription	Adipose Nuclei	Adipose
34	chr6:28093400-28094600	Weak transcription	Fetal Intestine Large	intestine
35	chr6:28093400-28094800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:28093400-28095400	Strong transcription	Colon Smooth Muscle	Colon
37	chr6:28093400-28096200	Weak transcription	Placenta	Placenta
38	chr6:28093400-28096200	Weak transcription	A549	lung
39	chr6:28093400-28096400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:28093400-28096400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr6:28093400-28098200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:28093400-28100600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:28093400-28102600	Weak transcription	NHDF-Ad	bronchial
44	chr6:28093400-28103200	Weak transcription	NHEK	skin
45	chr6:28093400-28103400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:28093600-28094600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:28093600-28094600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:28093600-28094800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr6:28093600-28094800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:28093600-28094800	Genic enhancers	HepG2	liver

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