Variant report

Variant	rs9806241
Chromosome Location	chr15:75779555-75779556
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	chr15:75743484..75746288-chr15:75777590..75779604,2	K562	blood:
2	chr15:75743324..75745076-chr15:75777150..75780089,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10851882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs11072544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs11072552	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1128933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs11632105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs11632813	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11634402	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs11636031	0.89[GIH][hapmap]
rs11636199	0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap]
rs11637263	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11638974	0.83[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs11853141	0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs11855087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12101874	0.88[CEU][hapmap]
rs12324230	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12708519	0.89[GIH][hapmap]
rs12708520	0.83[CHB][hapmap]
rs12903362	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909709	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911512	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915221	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916256	0.90[EUR][1000 genomes]
rs13380103	0.83[CHB][hapmap]
rs28376842	0.81[EUR][1000 genomes]
rs28610581	0.89[GIH][hapmap]
rs28693593	0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap]
rs28783769	0.84[GIH][hapmap]
rs3809549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs4075522	0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap]
rs4299117	0.89[GIH][hapmap]
rs4319732	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4322627	0.89[GIH][hapmap]
rs4408507	0.82[EUR][1000 genomes]
rs4430707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4451914	0.83[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap]
rs4462560	0.83[CHB][hapmap]
rs4526985	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4564532	0.83[CHB][hapmap]
rs4886442	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886443	0.87[GIH][hapmap]
rs4886446	0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap]
rs4886449	0.86[EUR][1000 genomes]
rs4886452	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4886699	0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap]
rs4886702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886703	0.83[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap]
rs4886704	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes]
rs4886705	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.95[EUR][1000 genomes]
rs4886706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886708	0.83[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap]
rs4886718	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs4886722	0.85[GIH][hapmap]
rs6495172	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495173	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495174	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs6495176	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495178	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495181	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495182	0.89[GIH][hapmap]
rs7163783	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7163907	0.87[GIH][hapmap]
rs7164541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165292	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165469	0.86[EUR][1000 genomes]
rs7166737	0.83[CHB][hapmap]
rs7170660	0.88[EUR][1000 genomes]
rs7173220	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175139	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7175852	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs7176989	0.91[EUR][1000 genomes]
rs7182283	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs73436868	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8023815	0.89[GIH][hapmap]
rs8026113	0.88[CEU][hapmap]
rs8028277	0.83[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap]
rs8029112	0.89[GIH][hapmap]
rs8030802	0.89[GIH][hapmap]
rs8034317	0.83[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap]
rs8038760	0.80[GIH][hapmap]
rs8043300	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	nsv482802	chr15:75686519-75899896	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
8	nsv904387	chr15:75706296-75806911	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	nsv904388	chr15:75730182-75804543	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	nsv904389	chr15:75739824-75806911	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv827390	chr15:75766087-75795370	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9806241	RCN2	cis	cerebellum	SCAN
rs9806241	MAN2C1	cis	Whole Blood	GTEx
rs9806241	PSTPIP1	cis	parietal	SCAN
rs9806241	MAN2C1	cis	cerebellum	SCAN
rs9806241	SNUPN	cis	parietal	SCAN
rs9806241	MAN2C1	cis	Nerve Tibial	GTEx
rs9806241	EDC3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75749000-75797800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:75749200-75782000	Weak transcription	Right Atrium	heart
3	chr15:75761600-75785200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:75762200-75798000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:75762400-75792000	Weak transcription	Esophagus	oesophagus
6	chr15:75762400-75797800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:75762400-75798000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:75763400-75780000	Weak transcription	Pancreas	Pancrea
9	chr15:75763600-75785800	Weak transcription	Psoas Muscle	Psoas
10	chr15:75763800-75779800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:75763800-75797800	Weak transcription	Brain Substantia Nigra	brain
12	chr15:75764200-75781600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr15:75765600-75797800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:75766800-75798000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:75767200-75784800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:75768200-75783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:75771000-75779800	Weak transcription	Lung	lung
18	chr15:75771200-75779600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:75771400-75781600	Weak transcription	Brain Anterior Caudate	brain
20	chr15:75771400-75782400	Weak transcription	Aorta	Aorta
21	chr15:75772000-75779800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:75772000-75797800	Weak transcription	NHEK	skin
23	chr15:75772200-75779800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:75772200-75779800	Weak transcription	Thymus	Thymus
25	chr15:75772200-75781600	Weak transcription	Brain Angular Gyrus	brain
26	chr15:75772200-75781600	Weak transcription	K562	blood
27	chr15:75772200-75781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:75772200-75782200	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:75772200-75794200	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:75772400-75779600	Weak transcription	Colonic Mucosa	Colon
31	chr15:75772400-75779800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:75772400-75779800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:75772400-75779800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:75772400-75779800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:75772400-75779800	Weak transcription	NHLF	lung
36	chr15:75772400-75781600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:75772400-75797800	Weak transcription	Fetal Brain Male	brain
38	chr15:75772400-75797800	Weak transcription	Right Ventricle	heart
39	chr15:75772400-75797800	Weak transcription	Spleen	Spleen
40	chr15:75772400-75798000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:75772600-75785000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:75775200-75780600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:75775200-75783400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:75775200-75787200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:75775200-75788000	Strong transcription	Dnd41	blood
46	chr15:75775200-75789600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:75775200-75789800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr15:75775200-75795400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:75775200-75795400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr15:75775400-75780200	Strong transcription	Primary T cells from cord blood	blood

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