Variant report

Variant	rs10487575
Chromosome Location	chr7:4286302-4286303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:4266434..4268284-chr7:4284245..4288090,3	MCF-7	breast:
2	chr7:4281480..4283823-chr7:4284575..4286412,2	MCF-7	breast:
3	chr7:4280752..4283162-chr7:4283913..4286565,5	MCF-7	breast:
4	chr7:4285802..4287439-chr7:4291050..4292753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146555	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10951486	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs12386762	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12386764	0.85[CHD][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs12531029	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs12701504	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs12701516	0.88[EUR][1000 genomes]
rs13226493	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs13228974	0.88[EUR][1000 genomes]
rs13229094	0.95[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13231488	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13242033	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13247068	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs34177767	0.90[EUR][1000 genomes]
rs34670163	0.88[EUR][1000 genomes]
rs34861141	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34931244	0.82[ASN][1000 genomes]
rs35168770	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35399365	0.89[EUR][1000 genomes]
rs35527356	0.89[EUR][1000 genomes]
rs35863749	0.88[EUR][1000 genomes]
rs35913974	0.89[EUR][1000 genomes]
rs4723519	0.89[EUR][1000 genomes]
rs4723528	0.91[EUR][1000 genomes]
rs4723539	0.92[EUR][1000 genomes]
rs4723545	0.90[EUR][1000 genomes]
rs56250749	0.85[EUR][1000 genomes]
rs67819850	0.84[EUR][1000 genomes]
rs6946599	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6966643	0.93[EUR][1000 genomes]
rs71527479	0.82[EUR][1000 genomes]
rs7781965	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs929371	0.89[EUR][1000 genomes]
rs929372	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs929373	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs929374	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv464274	chr7:3955516-4613607	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv464275	chr7:3955516-4613607	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv464276	chr7:3955516-4613607	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv464277	chr7:3955516-4613607	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv464278	chr7:3955516-4613607	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv605939	chr7:3955516-4613607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv917252	chr7:4017819-4374090	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv527624	chr7:4027536-4424054	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv869540	chr7:4063875-4302040	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv518299	chr7:4116665-4286597	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv949581	chr7:4166659-4485938	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1820543	chr7:4167991-4286597	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv887341	chr7:4167991-4298625	Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv887342	chr7:4182850-4293524	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv1023367	chr7:4192258-4306053	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv887344	chr7:4211696-4393478	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1030157	chr7:4272488-4311316	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv1034970	chr7:4283468-4405875	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv538693	chr7:4283468-4405875	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	esv3358075	chr7:4285826-4290624	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10487575	WIPI2	cis	cerebellum	SCAN
rs10487575	C7orf50	cis	cerebellum	SCAN
rs10487575	SNX8	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4235800-4287200	Weak transcription	Gastric	stomach
2	chr7:4268000-4291800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:4275600-4287800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:4276600-4288600	Strong transcription	Aorta	Aorta
5	chr7:4278400-4287600	Weak transcription	Fetal Heart	heart
6	chr7:4278400-4296000	Weak transcription	Brain Germinal Matrix	brain
7	chr7:4280800-4287800	Weak transcription	Fetal Kidney	kidney
8	chr7:4282000-4288600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:4283200-4288400	Weak transcription	Brain Angular Gyrus	brain
10	chr7:4283600-4287600	ZNF genes & repeats	Spleen	Spleen
11	chr7:4283600-4288000	Weak transcription	Fetal Brain Male	brain
12	chr7:4284400-4288000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr7:4284400-4290600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:4284600-4286400	Weak transcription	Fetal Intestine Large	intestine
15	chr7:4284600-4286800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:4284600-4287400	Weak transcription	Fetal Muscle Leg	muscle
17	chr7:4284600-4288800	Weak transcription	Colon Smooth Muscle	Colon
18	chr7:4284800-4286400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:4284800-4287800	Weak transcription	Adipose Nuclei	Adipose
20	chr7:4285000-4286400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:4285000-4287600	Weak transcription	Fetal Intestine Small	intestine
22	chr7:4285000-4291200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:4285200-4286400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:4285200-4286400	Strong transcription	Fetal Stomach	stomach
25	chr7:4285200-4287800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr7:4285200-4290200	Weak transcription	Right Ventricle	heart
27	chr7:4285400-4287600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr7:4285600-4301200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:4285800-4287200	Weak transcription	Pancreas	Pancrea
30	chr7:4285800-4291000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:4286000-4287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr7:4286000-4287200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr7:4286000-4287800	Weak transcription	Fetal Brain Female	brain
34	chr7:4286200-4286600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:4286200-4287200	Enhancers	Fetal Lung	lung
36	chr7:4286200-4290800	Weak transcription	Stomach Smooth Muscle	stomach

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