Variant report

Variant	rs12301562
Chromosome Location	chr12:48484616-48484617
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48483931..48486907-chr12:48497076..48499177,2	MCF-7	breast:
2	chr12:48479485..48481585-chr12:48483681..48486532,2	K562	blood:
3	chr12:48483866..48486025-chr12:48500056..48502880,2	MCF-7	breast:
4	chr12:48482467..48486128-chr12:48498140..48501766,4	K562	blood:

Variant related genes	Relation type
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10128967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10128968	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506276	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs10506279	1.00[ASN][1000 genomes]
rs10875718	1.00[CHB][hapmap]
rs10875719	1.00[CHB][hapmap]
rs11574026	1.00[CHB][hapmap]
rs11830378	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs11835938	1.00[ASN][1000 genomes]
rs12297820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12316682	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122802	0.80[EUR][1000 genomes]
rs17224674	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs17224828	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs17225198	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17607800	0.81[CEU][hapmap]
rs17823193	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs17823415	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs17823565	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2228501	0.83[EUR][1000 genomes]
rs3936179	0.83[EUR][1000 genomes]
rs4075914	0.83[EUR][1000 genomes]
rs41291959	0.86[EUR][1000 genomes]
rs41291961	0.83[EUR][1000 genomes]
rs41291963	1.00[ASN][1000 genomes]
rs41291967	1.00[ASN][1000 genomes]
rs55682541	0.83[EUR][1000 genomes]
rs55707383	0.87[EUR][1000 genomes]
rs55752728	0.83[EUR][1000 genomes]
rs55820056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55886138	0.81[EUR][1000 genomes]
rs55953382	0.87[EUR][1000 genomes]
rs56049209	0.86[EUR][1000 genomes]
rs56288528	0.83[EUR][1000 genomes]
rs56345199	0.87[AMR][1000 genomes]
rs57956448	1.00[ASN][1000 genomes]
rs58317398	1.00[ASN][1000 genomes]
rs60209369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60679254	1.00[ASN][1000 genomes]
rs7297558	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7301153	0.81[CEU][hapmap]
rs7301509	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7307874	0.81[CEU][hapmap]
rs7310935	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs73304917	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089110	1.00[ASN][1000 genomes]
rs74089159	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089163	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630296	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12301562	ZNF641	cis	multi-tissue	Pritchard
rs12301562	NCKAP5L	cis	parietal	SCAN
rs12301562	ZNF641	cis	Whole Blood	GTEx
rs12301562	DDN	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:48465000-48487400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
10	chr12:48470800-48492800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:48471400-48492000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:48472200-48489400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48472400-48492000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:48472600-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:48472600-48490200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr12:48472600-48490200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:48472600-48493600	Strong transcription	Fetal Thymus	thymus
18	chr12:48472800-48493800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:48473000-48494800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:48473200-48486200	Strong transcription	Placenta	Placenta
21	chr12:48473200-48492000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:48473600-48490000	Strong transcription	Primary T cells from cord blood	blood
23	chr12:48473600-48495400	Strong transcription	Dnd41	blood
24	chr12:48473800-48491600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr12:48473800-48492800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:48474000-48485600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:48474000-48493000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:48474000-48494800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:48474200-48485600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:48474200-48486200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:48474600-48492200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:48475000-48498200	Weak transcription	Psoas Muscle	Psoas
33	chr12:48476200-48485800	Strong transcription	HUVEC	blood vessel
34	chr12:48476400-48489400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
36	chr12:48477000-48484800	Strong transcription	A549	lung
37	chr12:48477200-48498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:48477400-48491200	Weak transcription	Fetal Kidney	kidney
39	chr12:48477400-48498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:48477800-48485800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:48477800-48489400	Weak transcription	HSMM	muscle
42	chr12:48478200-48489600	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:48478600-48486400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr12:48478600-48486800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:48478600-48492200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:48478600-48493600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:48478800-48485800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:48478800-48485800	Strong transcription	Adipose Nuclei	Adipose
49	chr12:48478800-48486200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:48478800-48486800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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