Variant report

Variant	rs3842985
Chromosome Location	chr12:121253747-121253748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121251970..121254055-chr12:121269166..121270703,2	K562	blood:
2	chr12:121252485..121255170-chr12:121340536..121342669,2	MCF-7	breast:
3	chr12:121253695..121256191-chr12:121282485..121284244,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213137	Chromatin interaction
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10774572	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10849791	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10849807	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065264	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065282	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065283	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065284	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065292	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065293	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065300	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065307	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11065311	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11608262	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11611087	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12371178	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12579868	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12580949	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12809299	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822123	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12825746	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12831094	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13746	0.82[ASN][1000 genomes]
rs1467283	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1542859	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1696357	0.80[EUR][1000 genomes]
rs2015462	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2047568	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393717	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2461475	0.91[ASN][1000 genomes]
rs2893876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213566	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3213567	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3213570	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3213572	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34009825	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34076777	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35706672	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35905305	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3809313	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3861797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3883901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3897746	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3901854	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4454799	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs471688	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4766979	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4766980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4767937	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs487943	0.81[ASN][1000 genomes]
rs494632	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs508595	0.83[ASN][1000 genomes]
rs520753	0.81[ASN][1000 genomes]
rs525425	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs531782	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs533264	0.81[ASN][1000 genomes]
rs534415	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs548452	0.82[ASN][1000 genomes]
rs572016	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs577961	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs580240	0.83[ASN][1000 genomes]
rs58291418	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58918988	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs590625	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs602984	0.80[ASN][1000 genomes]
rs608394	0.83[ASN][1000 genomes]
rs609700	0.81[ASN][1000 genomes]
rs610694	0.81[ASN][1000 genomes]
rs618482	0.83[ASN][1000 genomes]
rs624216	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625228	0.94[ASN][1000 genomes]
rs647881	0.81[ASN][1000 genomes]
rs661647	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs665585	0.82[ASN][1000 genomes]
rs666976	0.80[ASN][1000 genomes]
rs668622	0.82[ASN][1000 genomes]
rs7137504	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7305849	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73413868	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73415734	0.80[EUR][1000 genomes]
rs7969140	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs869781	0.81[EUR][1000 genomes]
rs909053	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9431	0.83[ASN][1000 genomes]
rs989986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989987	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3842985	SPPL3	cis	Nerve Tibial	GTEx
rs3842985	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs3842985	SPPL3	cis	Adipose Subcutaneous	GTEx
rs3842985	ACADS	cis	Thyroid	GTEx

Chromatin state (count:79 , 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	chr12:121222600-121259000	Weak transcription	Ovary	ovary
4	chr12:121222600-121260800	Weak transcription	Spleen	Spleen
5	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
6	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:121230000-121255200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:121234000-121264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:121234600-121263000	Weak transcription	A549	lung
10	chr12:121236400-121259000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:121237000-121255400	Weak transcription	Fetal Heart	heart
12	chr12:121237800-121255600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:121239200-121255000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:121239200-121260600	Weak transcription	Right Atrium	heart
15	chr12:121239400-121255200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:121239600-121255200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:121239800-121255200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:121240800-121260800	Weak transcription	Small Intestine	intestine
19	chr12:121241000-121261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:121241200-121258400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:121241200-121259000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:121241800-121255600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:121241800-121255800	Weak transcription	Primary T cells from cord blood	blood
24	chr12:121241800-121260800	Weak transcription	Thymus	Thymus
25	chr12:121242400-121259000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:121242600-121256400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:121244800-121264000	Weak transcription	Aorta	Aorta
28	chr12:121248000-121255000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:121248000-121255200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:121248000-121255600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:121248000-121264400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:121248000-121265200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:121248200-121255600	Weak transcription	Fetal Intestine Small	intestine
34	chr12:121248200-121267200	Weak transcription	Fetal Stomach	stomach
35	chr12:121248200-121272200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:121248400-121254800	Weak transcription	Placenta	Placenta
37	chr12:121248400-121266800	Weak transcription	Fetal Intestine Large	intestine
38	chr12:121248600-121255000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:121248600-121255200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:121248600-121255600	Weak transcription	Left Ventricle	heart
41	chr12:121248600-121255800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:121248600-121260200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:121248600-121267200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:121248800-121255000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:121248800-121255400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:121248800-121256000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:121248800-121259000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:121248800-121260600	Weak transcription	Fetal Thymus	thymus
49	chr12:121248800-121268600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr12:121248800-121270400	Weak transcription	Primary B cells from cord blood	blood

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