Variant report

Variant	rs708242
Chromosome Location	chr12:49334044-49334045
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr12:49333866-49334310	HL-60	blood:	n/a	chr12:49334264-49334277 chr12:49334090-49334103 chr12:49334092-49334101

No.	Distal block	Cell Line	Cell type
1	chr12:49333826..49338604-chr12:49339041..49343164,6	K562	blood:
2	chr12:49258244..49260897-chr12:49333538..49336282,2	MCF-7	breast:
3	chr12:49324577..49326698-chr12:49333742..49335694,2	K562	blood:

Variant related genes	Relation type
ENSG00000255863	TF binding region
ENSG00000172602	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11168810	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12122	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12829682	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2694841	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41291977	1.00[EUR][1000 genomes]
rs71464944	0.86[EUR][1000 genomes]
rs7305811	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7967350	0.87[AFR][1000 genomes]
rs7981004	0.81[ASW][hapmap]
rs833823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs833825	0.88[AMR][1000 genomes]
rs833829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs833830	0.81[ASW][hapmap]
rs833834	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs833835	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs863855	0.81[ASW][hapmap]
rs941193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv899067	chr12:49329695-49344508	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49314400-49338000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:49314400-49338600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:49319200-49349800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:49319400-49337800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:49319600-49334600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:49319800-49349400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:49320800-49335800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:49320800-49336000	Strong transcription	A549	lung
9	chr12:49320800-49338600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:49321000-49334200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:49321000-49335000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:49321000-49335600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:49321000-49335800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:49321000-49336400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:49321000-49336800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:49321000-49338200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:49321400-49334200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:49321600-49334600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:49321800-49337800	Strong transcription	Fetal Intestine Small	intestine
20	chr12:49322800-49335200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr12:49322800-49337600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:49322800-49338600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:49323000-49334600	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:49323000-49335200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:49323000-49335400	Strong transcription	Lung	lung
26	chr12:49323000-49335800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:49323000-49335800	Strong transcription	Adipose Nuclei	Adipose
28	chr12:49323000-49335800	Strong transcription	Fetal Brain Female	brain
29	chr12:49323000-49336400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr12:49323000-49337800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:49323000-49338600	Strong transcription	GM12878-XiMat	blood
32	chr12:49323200-49335800	Strong transcription	Brain Germinal Matrix	brain
33	chr12:49323200-49337800	Strong transcription	Fetal Intestine Large	intestine
34	chr12:49323400-49334800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr12:49323400-49335200	Strong transcription	HMEC	breast
36	chr12:49323400-49336400	Strong transcription	Hela-S3	cervix
37	chr12:49323400-49338600	Strong transcription	HUVEC	blood vessel
38	chr12:49324000-49337800	Strong transcription	Fetal Stomach	stomach
39	chr12:49324400-49335000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:49324400-49335400	Strong transcription	Spleen	Spleen
41	chr12:49324400-49337600	Strong transcription	Placenta	Placenta
42	chr12:49324400-49338200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:49324600-49336200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:49325000-49335200	Strong transcription	Brain Hippocampus Middle	brain
45	chr12:49325000-49336800	Strong transcription	NHEK	skin
46	chr12:49325200-49335000	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr12:49325400-49334200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:49325400-49334600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:49327000-49335800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:49327200-49334400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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