Variant report

Variant	rs12524774
Chromosome Location	chr6:44100047-44100048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:44099490-44100558	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:44099789-44100059	GM12891	blood:	n/a	n/a
3	JUN	chr6:44099548-44103069	K562	blood:	n/a	chr6:44102133-44102141 chr6:44100938-44100952
4	POLR2A	chr6:44099449-44101712	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:44099593-44100598	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:44099462-44100088	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:44099546..44105774-chr6:44219938..44225862,7	K562	blood:
2	chr6:44092682..44101478-chr6:44189085..44198306,11	K562	blood:
3	chr6:44098855..44101234-chr6:44121944..44124290,2	MCF-7	breast:
4	chr6:44099197..44101362-chr6:44132923..44135789,2	K562	blood:
5	chr6:44098700..44101340-chr6:44230675..44233376,2	K562	blood:
6	chr6:44099724..44102557-chr6:44186726..44188523,2	K562	blood:
7	chr6:44098943..44101929-chr6:44117025..44119826,2	MCF-7	breast:
8	chr6:43597550..43599414-chr6:44098473..44101374,2	K562	blood:
9	chr6:44093355..44100261-chr6:44212966..44217093,13	K562	blood:
10	chr6:43592753..43594614-chr6:44099178..44101334,2	K562	blood:

No data

Variant related genes	Relation type
TMEM63B	TF binding region
MRPL14	TF binding region
ENSG00000172432	Chromatin interaction
ENSG00000157593	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000265700	Chromatin interaction
ENSG00000146232	Chromatin interaction
ENSG00000112759	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10456527	0.88[JPT][hapmap]
rs12527942	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12528844	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12529211	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539379	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16871581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16871592	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277127	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35174285	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57571893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58635644	0.89[EUR][1000 genomes]
rs60819581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72855955	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72855957	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72855965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72855987	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72855989	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72858115	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72858118	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72858121	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72858128	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72858131	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462962	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462935	chr6:44046143-44117607	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv603002	chr6:44046143-44117607	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44096400-44101200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:44096400-44106600	Weak transcription	Aorta	Aorta
3	chr6:44096600-44100600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:44096600-44100600	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:44096600-44100800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:44096600-44100800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:44096600-44101200	Weak transcription	Hela-S3	cervix
8	chr6:44096600-44101400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:44096600-44101400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:44096600-44102400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:44096600-44102400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:44096600-44102400	Weak transcription	HSMMtube	muscle
13	chr6:44096600-44103200	Weak transcription	Primary B cells from cord blood	blood
14	chr6:44096600-44107200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:44096600-44107400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:44096600-44119400	Weak transcription	Right Atrium	heart
17	chr6:44096800-44100200	Strong transcription	Fetal Stomach	stomach
18	chr6:44096800-44100400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:44096800-44100400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:44096800-44100400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:44096800-44100400	Weak transcription	Adipose Nuclei	Adipose
22	chr6:44096800-44100400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:44096800-44100400	Weak transcription	Fetal Lung	lung
24	chr6:44096800-44100600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:44096800-44100600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:44096800-44100600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:44096800-44100600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:44096800-44100600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:44096800-44100600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:44096800-44100600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:44096800-44100600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:44096800-44100600	Weak transcription	Osteobl	bone
33	chr6:44096800-44100800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:44096800-44100800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:44096800-44100800	Weak transcription	Brain Anterior Caudate	brain
36	chr6:44096800-44100800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:44096800-44100800	Weak transcription	Fetal Heart	heart
38	chr6:44096800-44100800	Weak transcription	Fetal Kidney	kidney
39	chr6:44096800-44100800	Weak transcription	Fetal Thymus	thymus
40	chr6:44096800-44100800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:44096800-44100800	Weak transcription	NHLF	lung
42	chr6:44096800-44101000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:44096800-44101000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr6:44096800-44101000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:44096800-44101000	Weak transcription	Brain Germinal Matrix	brain
46	chr6:44096800-44101000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:44096800-44101000	Weak transcription	Brain Substantia Nigra	brain
48	chr6:44096800-44101000	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:44096800-44101000	Weak transcription	Ovary	ovary
50	chr6:44096800-44101000	Weak transcription	Placenta Amnion	Placenta Amnion

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