Variant report

Variant	rs12510410
Chromosome Location	chr4:85866802-85866803
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	chr4:85844299..85846003-chr4:85865441..85868769,3	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10029496	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10856851	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10856852	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11097026	1.00[CEU][hapmap];0.90[MKK][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11097028	0.83[EUR][1000 genomes]
rs11730981	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732309	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11732347	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12498637	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12498787	0.88[EUR][1000 genomes]
rs12502559	0.80[EUR][1000 genomes]
rs12503215	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506456	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12511112	0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap]
rs12640378	0.87[EUR][1000 genomes]
rs12648852	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13109918	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13114115	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118671	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs13124246	0.89[EUR][1000 genomes]
rs13125323	0.81[EUR][1000 genomes]
rs13141322	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13148035	0.88[EUR][1000 genomes]
rs1484660	0.86[AMR][1000 genomes]
rs1508670	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs17009317	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs17009334	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs17009341	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2046402	0.85[AMR][1000 genomes]
rs2046404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2869216	0.82[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes]
rs28754901	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3098928	0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs34239067	0.87[EUR][1000 genomes]
rs34314581	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4131745	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4376130	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4383611	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4464556	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4470615	0.86[EUR][1000 genomes]
rs4533765	0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4590017	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4624645	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4626191	0.88[EUR][1000 genomes]
rs4634212	0.85[EUR][1000 genomes]
rs55871210	0.83[EUR][1000 genomes]
rs56194765	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58074983	0.82[EUR][1000 genomes]
rs6531777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531782	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531783	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs67045782	0.89[AMR][1000 genomes]
rs67624868	0.82[EUR][1000 genomes]
rs6815917	0.82[EUR][1000 genomes]
rs6820517	0.81[EUR][1000 genomes]
rs6833661	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6847067	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6847564	0.81[JPT][hapmap]
rs6847811	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6857555	0.86[AMR][1000 genomes]
rs6858666	0.82[ASW][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs71597394	0.80[EUR][1000 genomes]
rs72664934	0.86[AMR][1000 genomes]
rs72664952	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72664957	0.81[EUR][1000 genomes]
rs7654035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7661609	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7663580	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7675324	0.88[EUR][1000 genomes]
rs7682896	0.80[EUR][1000 genomes]
rs7685537	0.86[JPT][hapmap];0.96[MEX][hapmap]
rs7692223	0.86[JPT][hapmap]
rs7694949	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7699226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9684737	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9790649	0.87[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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv508295	chr4:85822802-85885027	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12510410	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85798800-85873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:85809000-85872800	Weak transcription	A549	lung
3	chr4:85845600-85882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:85849200-85876000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:85849600-85869600	Weak transcription	Aorta	Aorta
6	chr4:85851200-85876000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:85853400-85868800	Weak transcription	Placenta	Placenta
8	chr4:85858600-85868800	Weak transcription	Ovary	ovary
9	chr4:85859000-85869600	Weak transcription	Psoas Muscle	Psoas
10	chr4:85860600-85869200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:85860600-85869400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:85860600-85872800	Weak transcription	Esophagus	oesophagus
13	chr4:85860600-85877000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:85860800-85872800	Weak transcription	NH-A	brain
15	chr4:85861200-85872400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:85861200-85873600	Weak transcription	HUVEC	blood vessel
17	chr4:85861400-85869200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:85861400-85869200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:85863200-85869200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:85863400-85872600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:85863800-85867400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:85864200-85868800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:85864200-85872800	Weak transcription	HSMM	muscle
24	chr4:85864400-85869200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:85864400-85869600	Weak transcription	Fetal Lung	lung
26	chr4:85864400-85873200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:85864400-85876400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:85864400-85877200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:85864800-85870800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:85864800-85871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:85865000-85867000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:85865200-85867200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:85865200-85876000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:85865200-85886400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:85865800-85869200	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:85865800-85885400	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:85866000-85886200	Weak transcription	Fetal Intestine Small	intestine
38	chr4:85866200-85867200	Enhancers	Right Ventricle	heart
39	chr4:85866200-85867400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr4:85866200-85867600	Enhancers	Fetal Heart	heart
41	chr4:85866200-85867800	Enhancers	Adipose Nuclei	Adipose
42	chr4:85866400-85867000	Weak transcription	Brain Anterior Caudate	brain
43	chr4:85866400-85867600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr4:85866400-85869200	Weak transcription	Stomach Mucosa	stomach
45	chr4:85866400-85872000	Weak transcription	HMEC	breast
46	chr4:85866400-85872800	Weak transcription	Pancreas	Pancrea
47	chr4:85866400-85873200	Weak transcription	NHLF	lung
48	chr4:85866400-85879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:85866600-85867200	Weak transcription	Brain Substantia Nigra	brain
50	chr4:85866600-85869000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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