Variant report

Variant	rs12950699
Chromosome Location	chr17:45173662-45173663
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45162074..45163604-chr17:45171046..45173992,2	MCF-7	breast:
2	chr17:45169541..45171629-chr17:45172586..45174850,2	K562	blood:
3	chr17:45170129..45171669-chr17:45173350..45174934,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10514915	0.95[ASN][1000 genomes]
rs1052586	0.80[CEU][hapmap]
rs11079745	0.82[CEU][hapmap]
rs11079748	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079752	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11649887	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11653589	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs11654517	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658350	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869840	0.84[CEU][hapmap]
rs11871052	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11871364	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12603447	0.89[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs12939753	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12942936	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949929	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12950276	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1634260	0.95[ASN][1000 genomes]
rs197926	0.80[CEU][hapmap]
rs2007723	0.90[ASN][1000 genomes]
rs2316331	0.93[ASN][1000 genomes]
rs2317376	0.95[ASN][1000 genomes]
rs2873131	0.95[ASN][1000 genomes]
rs34038545	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34314554	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34710835	0.96[ASN][1000 genomes]
rs35721448	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851786	0.81[CEU][hapmap]
rs3851792	0.87[CEU][hapmap]
rs4074247	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4074249	1.00[CEU][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968253	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968286	0.84[CEU][hapmap]
rs4968301	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968304	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56362502	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6504622	0.84[CEU][hapmap]
rs7207418	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7214785	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7215573	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215903	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215907	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219544	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219899	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220777	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7222781	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736604	0.80[CEU][hapmap]
rs8068715	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs8077021	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9889451	0.91[ASN][1000 genomes]
rs9889762	0.84[CEU][hapmap]
rs9899078	0.95[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	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats 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 miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers 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 miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv21010	chr17:45125753-45177221	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv521632	chr17:45151549-45196190	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv908563	chr17:45158537-45230311	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv962456	chr17:45163689-45212872	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12950699	GOSR2	Cis_1M	lymphoblastoid	RTeQTL
rs12950699	GOSR2	cis	normal skin	skin_eQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45145000-45176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:45145000-45176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:45145000-45176800	Weak transcription	Lung	lung
4	chr17:45145200-45176600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr17:45145400-45176000	Weak transcription	Primary T cells from cord blood	blood
6	chr17:45148800-45175400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:45149000-45173800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr17:45149600-45175400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr17:45149600-45176800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:45150200-45174600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:45150600-45176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr17:45150600-45176800	Weak transcription	Left Ventricle	heart
13	chr17:45158600-45175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr17:45159200-45175600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr17:45163200-45176800	Weak transcription	Fetal Intestine Large	intestine
16	chr17:45163800-45175000	Weak transcription	HepG2	liver
17	chr17:45164600-45174000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr17:45164800-45176600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr17:45166200-45176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:45167600-45177000	Weak transcription	Spleen	Spleen
21	chr17:45168400-45176000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:45168400-45176800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr17:45168600-45176200	Weak transcription	NH-A	brain
24	chr17:45168800-45176800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr17:45169200-45176200	Weak transcription	Adipose Nuclei	Adipose
26	chr17:45170000-45174600	Weak transcription	Primary B cells from cord blood	blood
27	chr17:45170200-45176800	Weak transcription	Aorta	Aorta
28	chr17:45170400-45176000	Weak transcription	Ovary	ovary
29	chr17:45170400-45176200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:45170400-45176200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr17:45170600-45176400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:45170600-45176600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr17:45170800-45174800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:45170800-45174800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:45170800-45176200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr17:45170800-45176200	Weak transcription	A549	lung
37	chr17:45171000-45173800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:45171000-45173800	Weak transcription	Dnd41	blood
39	chr17:45171000-45174400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:45171000-45174600	Weak transcription	Brain Germinal Matrix	brain
41	chr17:45171000-45174800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr17:45171000-45175600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:45171000-45176000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:45171000-45176000	Weak transcription	NHEK	skin
45	chr17:45171000-45176200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr17:45171000-45176200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr17:45171000-45176200	Weak transcription	Brain Hippocampus Middle	brain
48	chr17:45171000-45176200	Weak transcription	Fetal Brain Female	brain
49	chr17:45171000-45176200	Weak transcription	Fetal Intestine Small	intestine
50	chr17:45171000-45176200	Weak transcription	Fetal Muscle Leg	muscle

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