Variant report

Variant	rs10980241
Chromosome Location	chr9:99799056-99799057
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:99774341..99777390-chr9:99797289..99801643,6	MCF-7	breast:
2	chr9:99791951..99794165-chr9:99796736..99799706,2	K562	blood:

Variant related genes	Relation type
ENSG00000196312	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10114720	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10115220	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10118886	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10118923	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10123754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10123757	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10453219	0.85[ASN][1000 genomes]
rs10739289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10739296	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10759389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759399	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10759400	1.00[CEU][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10759406	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10759417	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10759420	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10816926	1.00[CEU][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816951	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10816953	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10816962	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10816963	0.92[EUR][1000 genomes]
rs10816964	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10816981	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816984	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816994	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10817013	0.84[EUR][1000 genomes]
rs10980243	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10980326	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10980346	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12236690	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12377546	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13299111	0.85[ASN][1000 genomes]
rs15394	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16919034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16924211	0.82[JPT][hapmap]
rs34342973	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4367680	0.80[EUR][1000 genomes]
rs4501700	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4510972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743056	0.85[ASN][1000 genomes]
rs59995818	0.89[EUR][1000 genomes]
rs6477844	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7023974	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7035822	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038926	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7039198	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7852748	0.85[ASN][1000 genomes]
rs7857836	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7873286	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7875800	1.00[ASW][hapmap];0.93[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9792463	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053215	chr9:99483926-99824810	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv831661	chr9:99611968-99800592	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv428540	chr9:99722815-99863455	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1824305	chr9:99792208-99806169	Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1821221	chr9:99792208-99811206	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10980241	SLC35D2	cis	cerebellum	SCAN
rs10980241	HEMGN	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99791400-99799400	Weak transcription	NHEK	skin
2	chr9:99792600-99800000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:99792600-99800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:99792800-99799800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:99793200-99800600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:99793400-99799600	Weak transcription	Fetal Intestine Small	intestine
7	chr9:99794200-99800200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:99794400-99799800	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr9:99794400-99799800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:99794400-99799800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:99794600-99800000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:99794800-99800000	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr9:99795200-99799800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:99795400-99799800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:99795600-99800000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:99796800-99799400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:99797200-99799800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:99797200-99800600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:99797400-99799800	Weak transcription	HMEC	breast
20	chr9:99797400-99800400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:99798000-99799800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:99798400-99799400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:99798600-99800200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:99798800-99799600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:99799000-99799400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:99799000-99799600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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