Variant report

Variant	rs12947874
Chromosome Location	chr17:38259103-38259104
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	FOXA2	chr17:38259061-38259774	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38252517..38259251-chr17:38276179..38282890,16	MCF-7	breast:
2	chr17:38257297..38260164-chr17:38470426..38472629,2	MCF-7	breast:

Variant related genes	Relation type
NR1D1	TF binding region
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12941465	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12941497	0.92[ASN][1000 genomes]
rs12942647	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071570	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795424	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs939347	0.82[EUR][1000 genomes];0.96[ASN][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	nsv908221	chr17:38216522-38289003	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv520636	chr17:38254689-38264197	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
4	nsv528369	chr17:38256693-38289003	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12947874	MSL1	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38256800-38269800	Weak transcription	Aorta	Aorta
2	chr17:38257000-38259200	Weak transcription	Gastric	stomach
3	chr17:38257000-38261800	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr17:38257400-38259200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:38257400-38262000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:38257400-38267200	Enhancers	Fetal Muscle Trunk	muscle
7	chr17:38257400-38267200	Enhancers	Fetal Muscle Leg	muscle
8	chr17:38257400-38267400	Enhancers	Fetal Intestine Small	intestine
9	chr17:38257400-38267800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr17:38257400-38269600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:38257400-38269600	Enhancers	Fetal Thymus	thymus
12	chr17:38257600-38259200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:38257600-38259400	Weak transcription	Ovary	ovary
14	chr17:38257600-38260200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:38257600-38260800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr17:38257600-38261400	Enhancers	Pancreas	Pancrea
17	chr17:38257600-38262000	Weak transcription	Brain Germinal Matrix	brain
18	chr17:38257600-38262200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr17:38257600-38262800	Enhancers	Fetal Lung	lung
20	chr17:38257600-38263200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:38257600-38263600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr17:38257600-38263600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr17:38257600-38263800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr17:38257600-38264600	Enhancers	Psoas Muscle	Psoas
25	chr17:38257600-38265800	Enhancers	Thymus	Thymus
26	chr17:38257600-38267200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:38257600-38267400	Enhancers	Primary T cells from cord blood	blood
28	chr17:38257600-38267600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr17:38257600-38269600	Enhancers	Fetal Intestine Large	intestine
30	chr17:38257600-38269600	Enhancers	Placenta	Placenta
31	chr17:38257800-38259200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr17:38257800-38259200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr17:38257800-38259200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:38257800-38259200	Enhancers	Colonic Mucosa	Colon
35	chr17:38257800-38259200	Weak transcription	Right Atrium	heart
36	chr17:38257800-38259400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr17:38257800-38259400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr17:38257800-38259400	Weak transcription	Brain Anterior Caudate	brain
39	chr17:38257800-38259400	Weak transcription	Brain Substantia Nigra	brain
40	chr17:38257800-38259400	Enhancers	Colon Smooth Muscle	Colon
41	chr17:38257800-38259400	Enhancers	Duodenum Mucosa	Duodenum
42	chr17:38257800-38259400	Weak transcription	Fetal Brain Female	brain
43	chr17:38257800-38260600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr17:38257800-38260600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr17:38257800-38261000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr17:38257800-38261200	Enhancers	Brain Hippocampus Middle	brain
47	chr17:38257800-38263000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr17:38257800-38263800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:38257800-38266000	Enhancers	Stomach Mucosa	stomach
50	chr17:38258000-38259200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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