Variant report

Variant	rs988588
Chromosome Location	chr3:157054016-157054017
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156876376..156878675-chr3:157052120..157054386,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1027603	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10936085	0.94[CHB][hapmap]
rs10936086	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs10936087	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs12486427	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs12492874	0.82[EUR][1000 genomes]
rs12492929	0.83[EUR][1000 genomes]
rs12496879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12629552	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12636038	0.82[EUR][1000 genomes]
rs12638732	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs13087207	0.83[EUR][1000 genomes]
rs1456097	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1456105	0.82[EUR][1000 genomes]
rs1456106	0.82[EUR][1000 genomes]
rs1456108	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs1456110	0.83[CEU][hapmap]
rs1500916	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1500919	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500920	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545596	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1546261	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs1563420	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs1568609	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568612	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1585080	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1824058	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs1840668	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs1840673	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1869857	0.84[CEU][hapmap]
rs1869859	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1965246	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs2047649	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2085315	0.82[EUR][1000 genomes]
rs2088815	0.88[CHB][hapmap];0.81[TSI][hapmap]
rs2124497	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2168430	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2168431	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2305620	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs2305622	0.82[EUR][1000 genomes]
rs28638274	0.84[CEU][hapmap]
rs35004310	0.82[EUR][1000 genomes]
rs3816527	0.81[JPT][hapmap]
rs3816528	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4435581	0.83[EUR][1000 genomes]
rs4640512	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs4640513	0.84[CEU][hapmap]
rs4679793	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4680351	0.94[CHB][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs4680358	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680359	0.94[CHB][hapmap]
rs4680360	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4680367	0.81[JPT][hapmap]
rs6441121	0.89[CHB][hapmap]
rs6441124	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441126	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs6441127	0.84[EUR][1000 genomes]
rs6441128	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs6441129	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs6776647	0.94[CHB][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs6780399	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6801110	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6803628	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs722484	0.83[EUR][1000 genomes]
rs7614339	0.83[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap]
rs7617727	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs7618737	0.84[EUR][1000 genomes]
rs7623173	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7626884	0.81[JPT][hapmap]
rs7629293	0.82[EUR][1000 genomes]
rs7631556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7639254	0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs885094	0.96[ASN][1000 genomes]
rs924517	0.89[CHB][hapmap]
rs9857875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867618	0.89[CHB][hapmap]
rs9871290	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs9878474	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs9883103	0.84[CHB][hapmap]
rs9883822	0.83[ASN][1000 genomes]
rs988587	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs988588	SSR3	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157041000-157065600	Weak transcription	Pancreas	Pancrea
2	chr3:157048000-157054600	Enhancers	NHDF-Ad	bronchial
3	chr3:157048200-157057000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:157050400-157054800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:157050600-157054600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:157051000-157054200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:157051000-157054800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:157051000-157054800	Enhancers	NHLF	lung
9	chr3:157051000-157056200	Enhancers	HUVEC	blood vessel
10	chr3:157051400-157054200	Enhancers	HSMM	muscle
11	chr3:157051400-157054400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:157051600-157054800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:157051800-157054200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:157051800-157054600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:157052000-157054800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:157052400-157054400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:157052400-157054400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:157052600-157054200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:157052800-157054200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:157053000-157054200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:157053000-157054200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr3:157053000-157054400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr3:157053000-157054400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:157053000-157054400	Enhancers	NH-A	brain
25	chr3:157053200-157054400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:157053400-157054400	Enhancers	H9 Cell Line	embryonic stem cell
27	chr3:157053400-157054400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:157053400-157054600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:157053400-157054600	Flanking Active TSS	A549	lung
30	chr3:157053600-157054600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:157053600-157054600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:157053800-157054200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:157053800-157055200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:157054000-157054200	Enhancers	Brain Anterior Caudate	brain
35	chr3:157054000-157054200	Enhancers	Brain Substantia Nigra	brain
36	chr3:157054000-157054200	Flanking Active TSS	Osteobl	bone
37	chr3:157054000-157054400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:157054000-157054400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:157054000-157054600	Enhancers	Brain Hippocampus Middle	brain

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