Variant report

Variant	rs7164541
Chromosome Location	chr15:75790644-75790645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

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];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs11072544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs11072552	0.96[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11632813	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11634402	0.96[CEU][hapmap];0.95[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	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11638974	0.83[CHB][hapmap];0.87[GIH][hapmap]
rs11853141	0.87[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs11855087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs12101874	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs12324230	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12708519	0.89[GIH][hapmap]
rs12708520	0.83[CHB][hapmap]
rs12903362	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909709	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12911512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915221	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916256	0.91[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4075522	0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap]
rs4299117	0.89[GIH][hapmap]
rs4319732	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4322627	0.89[GIH][hapmap]
rs4408507	0.82[EUR][1000 genomes]
rs4430707	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4451914	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs4462560	0.83[CHB][hapmap]
rs4526985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4564532	0.83[CHB][hapmap]
rs4886442	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886443	0.86[GIH][hapmap]
rs4886446	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap]
rs4886449	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886450	0.80[EUR][1000 genomes]
rs4886452	0.88[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs4886699	0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap]
rs4886702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886703	0.83[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap]
rs4886704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4886705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs4886706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.90[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];0.95[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4886722	0.87[GIH][hapmap]
rs6495172	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495173	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs6495176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495178	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6495182	0.89[GIH][hapmap]
rs7163783	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7163907	0.87[GIH][hapmap]
rs7165292	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165469	0.85[EUR][1000 genomes]
rs7166737	0.83[CHB][hapmap]
rs7170660	0.87[EUR][1000 genomes]
rs7173220	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175139	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7175852	0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap]
rs7176989	0.92[EUR][1000 genomes]
rs7182283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs73436868	0.99[AMR][1000 genomes];0.99[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]
rs8043300	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9806241	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]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7164541	SNUPN	cis	parietal	SCAN
rs7164541	MAN2C1	cis	cerebellum	SCAN
rs7164541	PSTPIP1	cis	parietal	SCAN
rs7164541	MAN2C1	cis	Nerve Tibial	GTEx
rs7164541	RCN2	cis	cerebellum	SCAN
rs7164541	EDC3	cis	cerebellum	SCAN

Chromatin state (count:124 , 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	chr15:75762200-75798000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr15:75762400-75792000	Weak transcription	Esophagus	oesophagus
4	chr15:75762400-75797800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:75762400-75798000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:75763800-75797800	Weak transcription	Brain Substantia Nigra	brain
7	chr15:75765600-75797800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:75766800-75798000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:75772000-75797800	Weak transcription	NHEK	skin
10	chr15:75772200-75794200	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:75772400-75797800	Weak transcription	Fetal Brain Male	brain
12	chr15:75772400-75797800	Weak transcription	Right Ventricle	heart
13	chr15:75772400-75797800	Weak transcription	Spleen	Spleen
14	chr15:75772400-75798000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:75775200-75795400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:75775200-75795400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr15:75775400-75795400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:75775800-75798000	Weak transcription	Fetal Heart	heart
19	chr15:75776000-75795400	Strong transcription	Fetal Stomach	stomach
20	chr15:75776200-75795400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:75777200-75792000	Weak transcription	Gastric	stomach
22	chr15:75777200-75794200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:75777200-75816800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:75777400-75794000	Weak transcription	HUVEC	blood vessel
25	chr15:75777600-75795400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:75777600-75812000	Weak transcription	Small Intestine	intestine
27	chr15:75778400-75795400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:75779000-75795000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:75779000-75795200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:75780200-75794600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:75780200-75797800	Weak transcription	Colonic Mucosa	Colon
32	chr15:75780200-75812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:75780600-75797800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:75781000-75797800	Weak transcription	Pancreas	Pancrea
35	chr15:75782000-75794800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr15:75782000-75797800	Weak transcription	Left Ventricle	heart
37	chr15:75782600-75793600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:75782600-75797800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:75782600-75797800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:75782600-75797800	Weak transcription	NHDF-Ad	bronchial
41	chr15:75782600-75815200	Weak transcription	K562	blood
42	chr15:75782800-75791400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:75782800-75791600	Weak transcription	Brain Anterior Caudate	brain
44	chr15:75782800-75793400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:75782800-75794000	Weak transcription	Fetal Thymus	thymus
46	chr15:75782800-75794200	Weak transcription	Ovary	ovary
47	chr15:75782800-75797800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:75782800-75797800	Weak transcription	Placenta	Placenta
49	chr15:75782800-75797800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:75782800-75797800	Weak transcription	GM12878-XiMat	blood

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