Variant report

Variant	rs2062507
Chromosome Location	chr12:121259051-121259052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121254206..121257153-chr12:121257780..121260885,3	MCF-7	breast:
2	chr12:121257951..121260496-chr12:121261739..121263322,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10774572	0.85[CEU][hapmap]
rs10849791	0.85[CEU][hapmap]
rs10849807	0.85[CEU][hapmap]
rs11065282	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs11065283	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs11065292	0.85[CEU][hapmap]
rs11065300	0.85[CEU][hapmap]
rs11065301	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11065311	0.85[CEU][hapmap]
rs11065324	0.85[CEU][hapmap]
rs12580949	0.87[CEU][hapmap]
rs12822123	0.84[CEU][hapmap]
rs12824150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1542859	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs1696357	0.85[CEU][hapmap]
rs2047568	0.85[CEU][hapmap]
rs3213570	0.88[CEU][hapmap]
rs3213572	0.85[CEU][hapmap]
rs3883901	0.84[CEU][hapmap]
rs3897746	0.85[CEU][hapmap]
rs3901854	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs4454799	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs4767935	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4767937	0.85[CEU][hapmap]
rs7137504	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs869781	0.85[CEU][hapmap]
rs909053	0.85[CEU][hapmap]
rs989986	0.85[CEU][hapmap]

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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2062507	SPPL3	cis	Nerve Tibial	GTEx
rs2062507	SPPL3	cis	Adipose Subcutaneous	GTEx
rs2062507	WSB2	cis	cerebellum	SCAN
rs2062507	MLEC	cis	lymphoblastoid	seeQTL
rs2062507	HPD	cis	parietal	SCAN
rs2062507	SPPL3	cis	cerebellum	SCAN
rs2062507	SPPL3	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121211400-121260800	Weak transcription	Gastric	stomach
2	chr12:121222200-121274000	Weak transcription	Lung	lung
3	chr12:121222600-121260800	Weak transcription	Spleen	Spleen
4	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
5	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:121234000-121264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:121234600-121263000	Weak transcription	A549	lung
8	chr12:121239200-121260600	Weak transcription	Right Atrium	heart
9	chr12:121240800-121260800	Weak transcription	Small Intestine	intestine
10	chr12:121241000-121261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:121241800-121260800	Weak transcription	Thymus	Thymus
12	chr12:121244800-121264000	Weak transcription	Aorta	Aorta
13	chr12:121248000-121264400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:121248000-121265200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:121248200-121267200	Weak transcription	Fetal Stomach	stomach
16	chr12:121248200-121272200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:121248400-121266800	Weak transcription	Fetal Intestine Large	intestine
18	chr12:121248600-121260200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:121248600-121267200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:121248800-121260600	Weak transcription	Fetal Thymus	thymus
21	chr12:121248800-121268600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:121248800-121270400	Weak transcription	Primary B cells from cord blood	blood
23	chr12:121248800-121271600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:121248800-121271800	Weak transcription	Dnd41	blood
25	chr12:121250800-121266600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr12:121253000-121260400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:121253200-121260600	Weak transcription	Fetal Kidney	kidney
28	chr12:121253800-121268600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:121254000-121268600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:121255200-121261600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:121255800-121270000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:121256000-121259400	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:121256000-121259600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:121256000-121261200	Weak transcription	Adipose Nuclei	Adipose
35	chr12:121256000-121266200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:121256000-121267200	Weak transcription	Placenta	Placenta
37	chr12:121256200-121260600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:121256400-121260400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:121256400-121260600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:121256600-121259200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:121256600-121260400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:121256600-121260600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:121256600-121260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:121256800-121259800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:121257000-121259400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:121257000-121260400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:121257000-121261600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr12:121257200-121259200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:121257200-121259800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:121257800-121259200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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