Variant report

Variant	rs1969017
Chromosome Location	chr12:117177864-117177865
allele	A/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	RFX5	chr12:117174654-117177903	SK-N-SH	brain:	n/a	chr12:117174964-117174973 chr12:117174962-117174976 chr12:117176118-117176127

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117172847..117175842-chr12:117176495..117179141,3	MCF-7	breast:
2	chr12:117172693..117174490-chr12:117177320..117180266,3	MCF-7	breast:

Variant related genes	Relation type
C12orf49	TF binding region
ENSG00000111412	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10850707	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068167	0.81[AFR][1000 genomes]
rs339454	0.81[AFR][1000 genomes]
rs339455	0.81[AFR][1000 genomes]
rs339456	0.81[AFR][1000 genomes]
rs339459	0.81[AFR][1000 genomes]
rs4767443	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138403	0.80[EUR][1000 genomes]
rs7296142	0.80[EUR][1000 genomes]
rs7312638	0.80[EUR][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	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1048004	chr12:117170738-117219076	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv1039046	chr12:117170989-117225635	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117176400-117179200	Weak transcription	Pancreas	Pancrea
2	chr12:117176600-117178000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:117176600-117179000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:117176600-117179200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:117176600-117179800	Weak transcription	Gastric	stomach
6	chr12:117176600-117181400	Weak transcription	Fetal Intestine Small	intestine
7	chr12:117176600-117197600	Weak transcription	Aorta	Aorta
8	chr12:117176600-117197800	Weak transcription	Right Atrium	heart
9	chr12:117176800-117178200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:117176800-117179400	Weak transcription	Fetal Kidney	kidney
11	chr12:117176800-117182200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:117176800-117182200	Weak transcription	Fetal Stomach	stomach
13	chr12:117176800-117197600	Weak transcription	Thymus	Thymus
14	chr12:117176800-117217400	Weak transcription	Primary T cells from cord blood	blood
15	chr12:117177000-117178000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:117177000-117178400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:117177000-117178400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:117177000-117178400	Weak transcription	Primary B cells from cord blood	blood
19	chr12:117177000-117178400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:117177000-117180600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:117177000-117181400	Weak transcription	Fetal Thymus	thymus
22	chr12:117177000-117182200	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:117177000-117187800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:117177000-117209400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:117177000-117217400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:117177000-117224400	Weak transcription	Brain Substantia Nigra	brain
27	chr12:117177200-117178000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:117177200-117178000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:117177200-117178200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:117177200-117178200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:117177200-117178200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:117177200-117178200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:117177200-117178400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:117177200-117178400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:117177200-117178400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:117177200-117178400	Weak transcription	Fetal Brain Female	brain
37	chr12:117177200-117178600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:117177200-117178600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:117177200-117197600	Weak transcription	A549	lung
40	chr12:117177200-117216800	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:117177200-117221000	Weak transcription	Fetal Brain Male	brain
42	chr12:117177400-117178000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:117177400-117178200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:117177400-117225800	Weak transcription	HepG2	liver
45	chr12:117177600-117178000	Weak transcription	Brain Angular Gyrus	brain
46	chr12:117177600-117178200	Weak transcription	Dnd41	blood
47	chr12:117177600-117178400	Weak transcription	Brain Germinal Matrix	brain
48	chr12:117177600-117178600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:117177600-117180200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:117177600-117217000	Weak transcription	GM12878-XiMat	blood

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