Variant report

Variant	rs7168659
Chromosome Location	chr15:52016499-52016500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52015204..52021746-chr15:52024939..52031385,17	MCF-7	breast:
2	chr15:52015670..52018450-chr15:52021031..52024231,3	K562	blood:
3	chr10:123395216..123396212-chr15:52016350..52016937,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 181 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:180)

rs_ID	r²[population]
rs1001690	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1035737	1.00[CEU][hapmap]
rs10444798	0.82[AMR][1000 genomes]
rs10444823	0.85[AMR][1000 genomes]
rs10444824	0.85[EUR][1000 genomes]
rs10444825	0.86[EUR][1000 genomes]
rs10775145	0.81[CHB][hapmap];0.84[AMR][1000 genomes]
rs11049	1.00[CEU][hapmap]
rs11070864	0.83[AMR][1000 genomes]
rs11070865	1.00[CEU][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070866	0.93[EUR][1000 genomes]
rs11070867	0.93[EUR][1000 genomes]
rs11070868	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11070869	0.87[EUR][1000 genomes]
rs1133883	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap]
rs11630084	0.89[AMR][1000 genomes]
rs11630579	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11630943	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11631858	0.82[EUR][1000 genomes]
rs11632106	0.88[AMR][1000 genomes]
rs11636345	0.81[CHB][hapmap];0.85[AMR][1000 genomes]
rs11636869	0.82[EUR][1000 genomes]
rs11637876	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11638766	0.89[AMR][1000 genomes]
rs11638820	0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs12050524	0.82[EUR][1000 genomes]
rs12593708	1.00[CEU][hapmap]
rs12903500	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12903707	0.86[CHB][hapmap];0.85[AMR][1000 genomes]
rs12904413	0.87[EUR][1000 genomes]
rs12904900	0.86[EUR][1000 genomes]
rs12905283	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12908327	1.00[CEU][hapmap]
rs12912928	0.82[EUR][1000 genomes]
rs12913583	0.82[EUR][1000 genomes]
rs12915015	1.00[CEU][hapmap]
rs12915568	1.00[CEU][hapmap]
rs12917133	0.81[CHB][hapmap];0.83[AMR][1000 genomes]
rs1350174	0.85[AMR][1000 genomes]
rs1545602	0.89[AMR][1000 genomes]
rs17526463	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17526760	1.00[CEU][hapmap]
rs17610862	0.87[EUR][1000 genomes]
rs17611193	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17705732	0.81[CHB][hapmap]
rs1811326	0.86[CHB][hapmap]
rs1840708	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1863430	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1867984	0.82[CHB][hapmap]
rs1902430	0.85[AMR][1000 genomes]
rs1972689	0.86[CHB][hapmap]
rs1991267	0.85[CEU][hapmap]
rs2007335	1.00[CEU][hapmap]
rs2007355	0.96[CEU][hapmap]
rs2009972	0.89[CEU][hapmap]
rs2010026	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2011995	1.00[CEU][hapmap]
rs2034856	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2034857	0.81[CHB][hapmap];0.85[AMR][1000 genomes]
rs2034858	0.81[CHB][hapmap];0.85[AMR][1000 genomes]
rs2052705	1.00[CEU][hapmap]
rs2052706	1.00[CEU][hapmap]
rs2052708	1.00[CEU][hapmap]
rs2077743	0.85[AMR][1000 genomes]
rs2252831	1.00[CEU][hapmap]
rs2264339	0.81[CHB][hapmap]
rs2414117	0.85[AMR][1000 genomes]
rs2414119	0.81[AMR][1000 genomes]
rs2433217	1.00[CEU][hapmap]
rs2433221	0.96[CEU][hapmap]
rs2436655	1.00[CEU][hapmap]
rs2436656	1.00[CEU][hapmap]
rs2441780	1.00[CEU][hapmap]
rs2448946	1.00[CEU][hapmap]
rs2448950	1.00[CEU][hapmap]
rs2554305	0.81[CHB][hapmap]
rs2554307	0.81[CHB][hapmap]
rs2554308	0.82[CHB][hapmap]
rs2554314	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2554327	1.00[CEU][hapmap]
rs2554336	0.86[CHB][hapmap]
rs2554348	0.89[CEU][hapmap]
rs2554349	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2570228	0.86[CHB][hapmap]
rs2570233	0.82[CHB][hapmap]
rs2570239	1.00[CEU][hapmap]
rs2570241	1.00[CEU][hapmap]
rs2570258	0.86[CHB][hapmap]
rs2593173	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs2593181	0.83[CEU][hapmap]
rs2623254	0.81[CHB][hapmap]
rs2623271	1.00[CEU][hapmap]
rs2623281	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2623282	1.00[CEU][hapmap]
rs2623283	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs28699115	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2912186	1.00[CEU][hapmap]
rs2912189	1.00[CEU][hapmap]
rs2916169	1.00[CEU][hapmap]
rs2916172	1.00[CEU][hapmap]
rs2916176	1.00[CEU][hapmap]
rs2929423	1.00[CEU][hapmap]
rs2929424	1.00[CEU][hapmap]
rs2929425	1.00[CEU][hapmap]
rs2959285	1.00[CEU][hapmap]
rs2959298	1.00[CEU][hapmap]
rs3088312	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34504520	0.85[EUR][1000 genomes]
rs35270232	0.82[EUR][1000 genomes]
rs35391204	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs35823585	0.85[EUR][1000 genomes]
rs3751596	0.81[CHB][hapmap];0.81[AMR][1000 genomes]
rs3794530	0.81[AMR][1000 genomes]
rs3794532	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3794534	0.85[AMR][1000 genomes]
rs3794535	0.86[CHB][hapmap];0.85[AMR][1000 genomes]
rs3794536	0.85[AMR][1000 genomes]
rs3898905	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4238383	0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs4365237	0.91[EUR][1000 genomes]
rs4502160	0.89[AMR][1000 genomes]
rs4534783	0.82[AMR][1000 genomes]
rs4622456	0.85[AMR][1000 genomes]
rs4774602	0.81[CHB][hapmap];0.85[AMR][1000 genomes]
rs4775978	0.85[AMR][1000 genomes]
rs4775982	0.81[CHB][hapmap];0.85[AMR][1000 genomes]
rs4775983	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs55843525	0.80[AMR][1000 genomes]
rs56148956	0.85[EUR][1000 genomes]
rs56185947	0.81[EUR][1000 genomes]
rs6493518	0.89[AMR][1000 genomes]
rs6493519	0.85[AMR][1000 genomes]
rs6493520	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6493521	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs6493522	0.82[AMR][1000 genomes]
rs6493523	0.86[CHB][hapmap]
rs6493525	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6493526	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs689884	0.81[CHB][hapmap];0.87[AMR][1000 genomes]
rs7162176	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7162925	1.00[CEU][hapmap]
rs7163176	0.85[AMR][1000 genomes]
rs7163541	1.00[CEU][hapmap]
rs7164961	0.85[EUR][1000 genomes]
rs7165585	0.85[AMR][1000 genomes]
rs7166110	0.89[AMR][1000 genomes]
rs7166962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170091	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs7171459	0.85[AMR][1000 genomes]
rs7171516	0.84[EUR][1000 genomes]
rs7171796	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7173375	0.90[AMR][1000 genomes]
rs7174497	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7174808	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7175017	0.90[EUR][1000 genomes]
rs7178166	0.91[EUR][1000 genomes]
rs7178561	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7178776	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7178940	0.80[EUR][1000 genomes]
rs7179599	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7181540	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs7181553	0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs726158	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8024081	0.86[AMR][1000 genomes]
rs8024088	0.85[AMR][1000 genomes]
rs8024585	0.82[EUR][1000 genomes]
rs8024589	0.85[AMR][1000 genomes]
rs8025069	0.91[EUR][1000 genomes]
rs8026521	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8028258	0.85[AMR][1000 genomes]
rs8028486	0.82[EUR][1000 genomes]
rs8028890	0.85[AMR][1000 genomes]
rs8028922	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8033433	0.80[EUR][1000 genomes]
rs8035173	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[EUR][1000 genomes]
rs8038344	1.00[CEU][hapmap]
rs8040975	0.91[EUR][1000 genomes]
rs8040986	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs8041268	0.85[AMR][1000 genomes]
rs9944235	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7168659	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
3	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:51990000-52016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:51991400-52018800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:51992200-52018800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:51993600-52016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:51999800-52018200	Weak transcription	Fetal Stomach	stomach
9	chr15:52000800-52024000	Weak transcription	Gastric	stomach
10	chr15:52001000-52018600	Weak transcription	Pancreas	Pancrea
11	chr15:52002800-52016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:52004800-52018600	Weak transcription	Spleen	Spleen
13	chr15:52006400-52018400	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:52007000-52023400	Weak transcription	Brain Anterior Caudate	brain
15	chr15:52007600-52016800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:52007800-52016800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:52007800-52018200	Weak transcription	NHDF-Ad	bronchial
18	chr15:52008200-52023200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:52008400-52018400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:52008400-52023400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:52008800-52016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:52009000-52016600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:52010800-52018400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:52010800-52018400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:52011000-52017000	Weak transcription	Adipose Nuclei	Adipose
26	chr15:52011200-52018400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:52011200-52018600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:52011400-52016600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:52011400-52018800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:52011400-52023400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:52011600-52018400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:52011600-52023400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:52011800-52018200	Weak transcription	Hela-S3	cervix
34	chr15:52011800-52018200	Weak transcription	HMEC	breast
35	chr15:52012000-52016800	Strong transcription	Primary B cells from cord blood	blood
36	chr15:52012400-52016600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:52012400-52017000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:52012400-52017200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr15:52012400-52024200	Weak transcription	Fetal Lung	lung
40	chr15:52012800-52017000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr15:52012800-52017200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr15:52012800-52017200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr15:52012800-52018400	Weak transcription	Ovary	ovary
44	chr15:52013000-52017200	Strong transcription	Dnd41	blood
45	chr15:52013200-52017000	Strong transcription	GM12878-XiMat	blood
46	chr15:52013400-52016600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:52013400-52018600	Weak transcription	Lung	lung
48	chr15:52013400-52018800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:52013400-52023600	Weak transcription	Colonic Mucosa	Colon
50	chr15:52013600-52018400	Weak transcription	Esophagus	oesophagus

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