Variant report

Variant	rs3883901
Chromosome Location	chr12:121256520-121256521
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	chr12:121249369..121251387-chr12:121254840..121256936,2	MCF-7	breast:
2	chr12:121254206..121257153-chr12:121257780..121260885,3	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10774572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10849791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10849807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11065324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1151849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11608262	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11611087	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];1.00[JPT][hapmap]
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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12824150	0.84[CEU][hapmap]
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	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs1467283	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1542859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs2015462	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2047568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2062507	0.84[CEU][hapmap]
rs2393717	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3213567	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3213570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3213572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3842985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3861797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3897746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3901854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4454799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs4767935	0.84[CEU][hapmap]
rs4767937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs520753	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs525425	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];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	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs618482	0.83[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs647881	0.81[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs909053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs989986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3883901	ACADS	cis	Thyroid	GTEx
rs3883901	SPPL3	cis	Nerve Tibial	GTEx
rs3883901	SPPL3	cis	cerebellum	SCAN
rs3883901	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs3883901	SPPL3	cis	Adipose Subcutaneous	GTEx
rs3883901	HPD	cis	parietal	SCAN
rs3883901	SRRM4	cis	cerebellum	SCAN
rs3883901	SPPL3	cis	parietal	SCAN
rs3883901	WSB2	cis	cerebellum	SCAN

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	chr12:121234000-121264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:121234600-121263000	Weak transcription	A549	lung
9	chr12:121236400-121259000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:121239200-121260600	Weak transcription	Right Atrium	heart
11	chr12:121240800-121260800	Weak transcription	Small Intestine	intestine
12	chr12:121241000-121261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:121241200-121258400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:121241200-121259000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:121241800-121260800	Weak transcription	Thymus	Thymus
16	chr12:121242400-121259000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:121244800-121264000	Weak transcription	Aorta	Aorta
18	chr12:121248000-121264400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:121248000-121265200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:121248200-121267200	Weak transcription	Fetal Stomach	stomach
21	chr12:121248200-121272200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:121248400-121266800	Weak transcription	Fetal Intestine Large	intestine
23	chr12:121248600-121260200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:121248600-121267200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:121248800-121259000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:121248800-121260600	Weak transcription	Fetal Thymus	thymus
27	chr12:121248800-121268600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:121248800-121270400	Weak transcription	Primary B cells from cord blood	blood
29	chr12:121248800-121271600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr12:121248800-121271800	Weak transcription	Dnd41	blood
31	chr12:121249600-121259000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:121250800-121266600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:121253000-121256800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:121253000-121257000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:121253000-121260400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:121253200-121260600	Weak transcription	Fetal Kidney	kidney
37	chr12:121253800-121268600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:121254000-121258800	Weak transcription	GM12878-XiMat	blood
39	chr12:121254000-121268600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:121254800-121258000	Enhancers	Brain Hippocampus Middle	brain
41	chr12:121255000-121257200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr12:121255000-121258000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr12:121255000-121258200	Enhancers	Brain Substantia Nigra	brain
44	chr12:121255200-121256600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:121255200-121256600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr12:121255200-121257000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:121255200-121257200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:121255200-121258000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr12:121255200-121258000	Enhancers	Brain Cingulate Gyrus	brain
50	chr12:121255200-121261600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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