Variant report

Variant	rs9613777
Chromosome Location	chr22:29420482-29420483
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	chr22:29420060..29422045-chr22:29423425..29426418,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12484832	0.96[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12485244	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17440734	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1977047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983553	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2064084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072774	0.81[EUR][1000 genomes]
rs2103544	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2347789	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28541979	0.87[EUR][1000 genomes]
rs4140643	1.00[CEU][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4333023	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4404379	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4594553	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4616575	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs469994	0.92[CEU][hapmap]
rs4820794	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4823002	0.96[CEU][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4823003	0.96[CEU][hapmap]
rs4823005	0.96[CEU][hapmap]
rs5997427	0.83[MKK][hapmap];0.81[YRI][hapmap]
rs5997430	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997431	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997432	0.82[EUR][1000 genomes]
rs5997433	0.96[CEU][hapmap]
rs5997434	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997435	0.85[EUR][1000 genomes]
rs6005955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005959	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005964	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005965	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6005967	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66905312	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs713834	0.96[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs727892	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7284304	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7287517	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7290304	0.96[CEU][hapmap]
rs738246	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8137254	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8137499	0.92[CEU][hapmap]
rs8142591	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874915	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874916	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9608719	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9608720	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs9608721	0.86[EUR][1000 genomes]
rs9613768	0.89[CHD][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs9613771	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9613778	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9613780	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs9613782	0.82[CEU][hapmap];0.87[CHD][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs9613784	0.84[EUR][1000 genomes]
rs9613785	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs964589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9613777	GGT5	cis	parietal	SCAN
rs9613777	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29400600-29425400	Weak transcription	NHEK	skin
2	chr22:29401400-29425000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr22:29401800-29426200	Weak transcription	Colon Smooth Muscle	Colon
4	chr22:29405400-29424600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:29408200-29422600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr22:29410400-29424800	Weak transcription	Psoas Muscle	Psoas
7	chr22:29411000-29422200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr22:29412400-29424200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr22:29415200-29422000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:29415200-29424400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr22:29415200-29426200	Weak transcription	Aorta	Aorta
12	chr22:29417200-29420800	Enhancers	Fetal Intestine Small	intestine
13	chr22:29417200-29421000	Enhancers	Fetal Intestine Large	intestine
14	chr22:29417600-29420600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr22:29418200-29420800	Enhancers	Duodenum Mucosa	Duodenum
16	chr22:29418400-29420800	Enhancers	Fetal Kidney	kidney
17	chr22:29418600-29420600	Enhancers	Liver	Liver
18	chr22:29418600-29422600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr22:29418800-29420800	Enhancers	Adipose Nuclei	Adipose
20	chr22:29419000-29421000	Enhancers	HepG2	liver
21	chr22:29419200-29420600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr22:29419200-29420600	Enhancers	Brain Anterior Caudate	brain
23	chr22:29419200-29420600	Enhancers	Fetal Heart	heart
24	chr22:29419200-29420600	Enhancers	HUVEC	blood vessel
25	chr22:29419400-29420600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr22:29419400-29420600	Enhancers	Stomach Mucosa	stomach
27	chr22:29419600-29422200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:29419600-29424200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr22:29419600-29424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:29419600-29425000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr22:29419600-29425000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr22:29419600-29425000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr22:29419600-29425600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:29419600-29426000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr22:29419600-29426200	Weak transcription	HSMM	muscle
36	chr22:29419800-29422600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr22:29419800-29424600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr22:29419800-29424600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:29419800-29425400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr22:29419800-29425800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr22:29419800-29426000	Weak transcription	Fetal Muscle Leg	muscle
42	chr22:29419800-29426200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr22:29419800-29426200	Weak transcription	Ovary	ovary
44	chr22:29419800-29426200	Weak transcription	Right Atrium	heart
45	chr22:29420000-29423600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr22:29420000-29424000	Weak transcription	Fetal Lung	lung
47	chr22:29420000-29424200	Weak transcription	Fetal Stomach	stomach
48	chr22:29420000-29424400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr22:29420000-29424400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr22:29420000-29424400	Weak transcription	Rectal Mucosa Donor 29	rectum

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