Variant report

Variant	rs4368021
Chromosome Location	chr12:25401822-25401823
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	chr12:25400232..25401983-chr12:25402090..25403679,2	MCF-7	breast:
2	chr12:25400101..25402008-chr12:25403784..25406782,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133703	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10505959	0.90[JPT][hapmap]
rs10743548	0.87[EUR][1000 genomes]
rs10771174	0.81[JPT][hapmap]
rs10771175	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs10771176	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs10771183	0.87[EUR][1000 genomes]
rs10842468	0.88[JPT][hapmap]
rs10842470	1.00[JPT][hapmap]
rs10842490	1.00[JPT][hapmap]
rs10842515	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842516	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842517	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11047878	0.84[EUR][1000 genomes]
rs11047879	0.86[EUR][1000 genomes]
rs11047885	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11047903	0.92[EUR][1000 genomes]
rs11047904	0.92[EUR][1000 genomes]
rs11047912	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11047914	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047917	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1137282	0.91[EUR][1000 genomes]
rs11836509	0.91[EUR][1000 genomes]
rs12227966	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12228638	0.89[JPT][hapmap]
rs12367971	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs17388573	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17388587	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17389103	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2220196	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs3924650	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4313666	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4606562	0.92[EUR][1000 genomes]
rs61761150	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7134616	0.82[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7298444	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303373	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs7309670	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311692	0.95[ASN][1000 genomes]
rs7315339	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7960917	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7964623	0.86[EUR][1000 genomes]
rs7965763	0.85[EUR][1000 genomes]
rs7968023	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971062	0.89[JPT][hapmap]
rs7971288	0.89[JPT][hapmap]
rs7973450	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7973623	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs7976254	0.90[JPT][hapmap]
rs7976355	1.00[JPT][hapmap]
rs7977616	0.91[EUR][1000 genomes]
rs7980769	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7980834	0.91[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	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv898926	chr12:25367669-25408047	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv898927	chr12:25389220-25408047	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4368021	SSPN	cis	parietal	SCAN
rs4368021	SSPN	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
3	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
4	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
5	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:25350000-25402800	Weak transcription	Ovary	ovary
10	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:25354400-25402200	Weak transcription	Pancreas	Pancrea
12	chr12:25356600-25402600	Weak transcription	Fetal Heart	heart
13	chr12:25360800-25402200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:25361000-25402600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:25361000-25402600	Weak transcription	Fetal Brain Female	brain
16	chr12:25362000-25402400	Weak transcription	HepG2	liver
17	chr12:25372400-25402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:25374800-25402600	Weak transcription	Placenta	Placenta
19	chr12:25375000-25402800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:25377800-25402200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:25377800-25402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:25380400-25402200	Weak transcription	Fetal Lung	lung
23	chr12:25381200-25402400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:25382000-25402600	Weak transcription	Colonic Mucosa	Colon
25	chr12:25385200-25402600	Weak transcription	Aorta	Aorta
26	chr12:25386200-25402800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:25386400-25402800	Weak transcription	Gastric	stomach
28	chr12:25386600-25402600	Weak transcription	Fetal Kidney	kidney
29	chr12:25386800-25402600	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:25389000-25402200	Weak transcription	Right Atrium	heart
31	chr12:25389000-25402600	Weak transcription	HMEC	breast
32	chr12:25389200-25402000	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:25389400-25402200	Weak transcription	Psoas Muscle	Psoas
34	chr12:25389400-25402800	Weak transcription	Left Ventricle	heart
35	chr12:25389800-25402400	Weak transcription	NHEK	skin
36	chr12:25389800-25402600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:25389800-25402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:25389800-25402600	Weak transcription	HSMMtube	muscle
39	chr12:25390000-25402600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:25390600-25402000	Weak transcription	Lung	lung
41	chr12:25390600-25402200	Weak transcription	Esophagus	oesophagus
42	chr12:25390600-25402200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:25390600-25402600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:25390600-25402600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:25390600-25402600	Weak transcription	Fetal Stomach	stomach
46	chr12:25390800-25402800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:25391000-25402600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:25392000-25402200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:25392000-25402600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:25392000-25402800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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