Variant report

Variant	rs6955490
Chromosome Location	chr7:98974588-98974589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:98970407..98975516-chr7:99002028..99009396,17	MCF-7	breast:
2	chr7:98970545..98974719-chr7:98992685..98998543,7	MCF-7	breast:
3	chr7:98970980..98974747-chr7:98986775..98992580,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130429	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106244	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10155966	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap];0.84[EUR][1000 genomes]
rs10225529	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10238965	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs10243678	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap];0.82[EUR][1000 genomes]
rs10249167	0.82[EUR][1000 genomes]
rs10255399	0.86[EUR][1000 genomes]
rs10258757	0.92[ASW][hapmap];0.91[CEU][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs10268984	0.80[TSI][hapmap]
rs10270459	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10270917	0.91[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs10271049	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs10272998	0.83[ASW][hapmap];0.91[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs10274407	0.81[EUR][1000 genomes]
rs10277149	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10279308	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1043466	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs1045012	1.00[JPT][hapmap]
rs10953287	0.81[EUR][1000 genomes]
rs10953288	0.80[CEU][hapmap]
rs11762273	0.92[ASW][hapmap];0.91[CEU][hapmap];0.83[MKK][hapmap];0.86[EUR][1000 genomes]
rs11771702	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11972017	0.88[MEX][hapmap]
rs11976018	0.83[ASW][hapmap];0.84[CEU][hapmap];0.81[MKK][hapmap]
rs11977673	1.00[CHB][hapmap]
rs11978089	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12112936	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12113440	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12538893	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs17161662	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap]
rs17161669	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap]
rs17161695	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17161700	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17161726	1.00[JPT][hapmap]
rs17854665	1.00[JPT][hapmap]
rs1980307	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs2003499	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2057906	0.85[YRI][hapmap]
rs2072181	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2240384	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs2272168	0.84[CEU][hapmap]
rs2280600	0.84[CEU][hapmap]
rs2280601	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs2286162	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2293256	1.00[JPT][hapmap]
rs28377312	1.00[JPT][hapmap]
rs28495024	0.81[EUR][1000 genomes]
rs28558950	1.00[JPT][hapmap]
rs28668326	1.00[JPT][hapmap]
rs28820905	0.82[EUR][1000 genomes]
rs3137	0.84[CEU][hapmap]
rs3801288	0.91[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs41385645	1.00[JPT][hapmap]
rs4729532	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6943920	0.91[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap]
rs6953476	0.81[EUR][1000 genomes]
rs6957987	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6958704	0.83[EUR][1000 genomes]
rs6962772	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs6972337	0.81[EUR][1000 genomes]
rs6973408	0.83[EUR][1000 genomes]
rs6974831	1.00[JPT][hapmap]
rs6975099	0.81[EUR][1000 genomes]
rs733991	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7794705	0.84[CEU][hapmap]
rs7805661	1.00[JPT][hapmap]
rs883403	0.84[CEU][hapmap]
rs917152	1.00[JPT][hapmap]
rs917154	0.83[ASW][hapmap];0.83[CEU][hapmap];0.81[MKK][hapmap]
rs952319	1.00[JPT][hapmap]
rs9969217	0.88[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6955490	OR2AE1	cis	parietal	SCAN
rs6955490	GATS	cis	parietal	SCAN
rs6955490	CPSF4	cis	parietal	SCAN
rs6955490	PILRB	cis	lymphoblastoid	GTEx
rs6955490	ZKSCAN1	cis	parietal	SCAN
rs6955490	STAG3	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98970800-98977000	Weak transcription	Fetal Lung	lung
2	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
3	chr7:98973200-98978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:98973400-98974600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:98973400-98974600	Weak transcription	Spleen	Spleen
6	chr7:98973400-98974800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:98973400-98975000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:98973400-98975000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:98973400-98975000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:98973400-98975400	Enhancers	HMEC	breast
11	chr7:98973400-98975400	Weak transcription	Osteobl	bone
12	chr7:98973400-98975600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:98973400-98976600	Weak transcription	NH-A	brain
14	chr7:98973400-98976600	Weak transcription	NHLF	lung
15	chr7:98973400-98976800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:98973400-98976800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:98973400-98976800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:98973400-98976800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:98973400-98976800	Weak transcription	HSMM	muscle
20	chr7:98973400-98976800	Weak transcription	HSMMtube	muscle
21	chr7:98973400-98977000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr7:98973400-98977000	Weak transcription	Brain Anterior Caudate	brain
23	chr7:98973400-98977000	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:98973400-98977000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:98973400-98977000	Weak transcription	Esophagus	oesophagus
26	chr7:98973400-98977000	Weak transcription	Right Atrium	heart
27	chr7:98973400-98977200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr7:98973400-98977200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:98973400-98977200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr7:98973400-98977200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr7:98973400-98977600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:98973400-98977600	Weak transcription	Brain Substantia Nigra	brain
33	chr7:98973400-98977600	Weak transcription	Fetal Heart	heart
34	chr7:98973400-98977600	Weak transcription	Small Intestine	intestine
35	chr7:98973400-98978400	Weak transcription	Psoas Muscle	Psoas
36	chr7:98973400-98978600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:98973400-98978800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:98973400-98979000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:98973400-98979200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr7:98973400-98984000	Weak transcription	Aorta	Aorta
41	chr7:98973400-98984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:98973400-98984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:98973400-98984200	Weak transcription	Ovary	ovary
44	chr7:98973400-98984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
46	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
48	chr7:98973600-98974600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:98973600-98974600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:98973600-98974800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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