Variant report

Variant	rs973398
Chromosome Location	chr12:48491048-48491049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48490196..48492740-chr12:48498056..48500665,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10161358	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10875716	0.88[CEU][hapmap]
rs10875718	0.88[CEU][hapmap]
rs10875719	0.88[CEU][hapmap]
rs10875721	0.81[EUR][1000 genomes]
rs10875743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10875749	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10875753	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1107654	1.00[CHB][hapmap]
rs11168351	0.88[CEU][hapmap]
rs11168408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11168428	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168437	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11168441	1.00[CHB][hapmap]
rs11168460	1.00[CHB][hapmap]
rs12099462	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12228750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12368659	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12816820	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs1476607	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17122498	1.00[CHB][hapmap]
rs2051851	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2054905	1.00[CHB][hapmap]
rs3997	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4760612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs4760679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6580650	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6580652	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6580654	0.81[EUR][1000 genomes]
rs7139330	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7295580	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7297824	1.00[CHB][hapmap]
rs7301003	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7307566	1.00[CHB][hapmap]
rs7315820	1.00[CHB][hapmap]
rs7486941	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7487682	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7971880	0.88[CEU][hapmap]
rs7975632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs8716	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9971924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs973398	H1FNT	cis	Muscle Skeletal	GTEx
rs973398	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
7	chr12:48470800-48492800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:48471400-48492000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:48472400-48492000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:48472600-48493600	Strong transcription	Fetal Thymus	thymus
11	chr12:48472800-48493800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:48473000-48494800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:48473200-48492000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:48473600-48495400	Strong transcription	Dnd41	blood
15	chr12:48473800-48491600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:48473800-48492800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:48474000-48493000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:48474000-48494800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:48474600-48492200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:48475000-48498200	Weak transcription	Psoas Muscle	Psoas
21	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
22	chr12:48477200-48498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:48477400-48491200	Weak transcription	Fetal Kidney	kidney
24	chr12:48477400-48498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:48478600-48492200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:48478600-48493600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:48478800-48492000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:48478800-48492000	Strong transcription	Liver	Liver
29	chr12:48478800-48492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:48479400-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:48479400-48498200	Weak transcription	Brain Angular Gyrus	brain
32	chr12:48479400-48498400	Weak transcription	Aorta	Aorta
33	chr12:48479600-48498000	Weak transcription	NHEK	skin
34	chr12:48480000-48492800	Strong transcription	K562	blood
35	chr12:48480400-48498200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:48480800-48493600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:48481200-48493800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr12:48482800-48498200	Weak transcription	NHDF-Ad	bronchial
39	chr12:48483000-48498200	Weak transcription	NH-A	brain
40	chr12:48483000-48498400	Weak transcription	HSMMtube	muscle
41	chr12:48483200-48498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:48483200-48498200	Weak transcription	HepG2	liver
43	chr12:48483200-48498400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:48483200-48499200	Weak transcription	Small Intestine	intestine
45	chr12:48483400-48498200	Weak transcription	NHLF	lung
46	chr12:48484400-48491400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:48484400-48492400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr12:48484600-48492200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr12:48484800-48491200	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:48484800-48498200	Weak transcription	Muscle Satellite Cultured Cells	--

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