Variant report

Variant	rs6797664
Chromosome Location	chr3:49539222-49539223
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	chr3:49507792..49509395-chr3:49538517..49540372,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10212296	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1050088	0.94[ASN][1000 genomes]
rs1050450	0.83[AMR][1000 genomes]
rs10640	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10865955	0.82[ASN][1000 genomes]
rs11130199	0.94[ASN][1000 genomes]
rs11130202	0.94[ASN][1000 genomes]
rs11130203	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130206	0.84[ASN][1000 genomes]
rs11706370	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11708955	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11711485	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711536	0.81[AMR][1000 genomes]
rs11712569	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713474	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715915	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11716974	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11719996	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720264	0.94[ASN][1000 genomes]
rs11720458	0.86[ASN][1000 genomes]
rs11720597	0.86[EUR][1000 genomes]
rs11922013	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11926781	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12330269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488065	0.88[ASN][1000 genomes]
rs12489092	0.94[ASN][1000 genomes]
rs13062429	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13064576	0.84[EUR][1000 genomes]
rs13079082	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079643	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13087851	0.85[AMR][1000 genomes]
rs13090388	0.83[AMR][1000 genomes]
rs1568661	0.94[ASN][1000 genomes]
rs17080528	0.83[AMR][1000 genomes]
rs1800668	0.85[AMR][1000 genomes]
rs1801143	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987628	0.85[AMR][1000 genomes]
rs2312461	0.94[ASN][1000 genomes]
rs34196454	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34293138	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34363169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34427167	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34588335	0.83[AMR][1000 genomes]
rs35115732	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35169793	0.83[AMR][1000 genomes]
rs35261698	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35701831	0.94[ASN][1000 genomes]
rs35999162	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811697	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811699	0.83[AMR][1000 genomes]
rs3870337	0.94[ASN][1000 genomes]
rs3870338	0.94[ASN][1000 genomes]
rs3877784	0.94[ASN][1000 genomes]
rs3924462	0.94[ASN][1000 genomes]
rs3926569	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4241406	0.86[ASN][1000 genomes]
rs4625	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855836	0.94[ASN][1000 genomes]
rs4855855	0.85[ASN][1000 genomes]
rs4855859	0.94[ASN][1000 genomes]
rs4855861	0.94[ASN][1000 genomes]
rs4855864	0.94[ASN][1000 genomes]
rs4855866	0.80[ASN][1000 genomes]
rs56116382	0.87[ASN][1000 genomes]
rs62261185	0.81[ASN][1000 genomes]
rs6446264	0.85[AMR][1000 genomes]
rs6446272	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6446277	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67216675	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67485053	0.85[AMR][1000 genomes]
rs6766131	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779524	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6793308	0.83[AMR][1000 genomes]
rs6809216	0.83[AMR][1000 genomes]
rs6997	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71324962	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71615484	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7371895	0.82[ASN][1000 genomes]
rs7622302	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623659	0.83[AMR][1000 genomes]
rs7630869	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7633271	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637999	0.94[ASN][1000 genomes]
rs7643845	0.94[ASN][1000 genomes]
rs7646366	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7648841	0.85[AMR][1000 genomes]
rs885592	0.82[ASN][1000 genomes]
rs9814873	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9818590	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821311	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9827021	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837027	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9841110	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858280	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858418	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9859556	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9871380	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9875617	0.87[EUR][1000 genomes]
rs9878943	0.86[AMR][1000 genomes];0.82[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6797664	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs6797664	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs6797664	FAM212A	cis	Muscle Skeletal	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
6	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
7	chr3:49517000-49547800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:49517200-49547800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:49522200-49547800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:49522400-49548000	Weak transcription	Spleen	Spleen
11	chr3:49523400-49548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:49523400-49548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:49523600-49548200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:49526000-49547800	Weak transcription	Dnd41	blood
15	chr3:49526000-49548000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:49527600-49547800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:49528200-49539600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:49529600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:49530400-49547800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:49531000-49548000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:49531200-49547800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:49531400-49539600	Weak transcription	Fetal Stomach	stomach
23	chr3:49531400-49547600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:49531400-49547800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:49531400-49547800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:49531400-49547800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:49531600-49547800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:49531600-49547800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:49531600-49547800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:49531800-49539600	Weak transcription	Primary T cells from cord blood	blood
31	chr3:49531800-49547400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:49531800-49547800	Weak transcription	Brain Germinal Matrix	brain
33	chr3:49533000-49547800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:49533000-49547800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:49533000-49547800	Weak transcription	Ovary	ovary
36	chr3:49533000-49547800	Weak transcription	GM12878-XiMat	blood
37	chr3:49533200-49540400	Weak transcription	Primary B cells from cord blood	blood
38	chr3:49533200-49541000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:49533800-49547800	Weak transcription	Thymus	Thymus
40	chr3:49535200-49539600	Enhancers	Fetal Intestine Small	intestine
41	chr3:49535400-49539400	Enhancers	Fetal Muscle Leg	muscle
42	chr3:49535400-49539800	Enhancers	Fetal Intestine Large	intestine
43	chr3:49535600-49539600	Enhancers	Small Intestine	intestine
44	chr3:49536400-49539400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:49536600-49548000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:49536800-49540000	Enhancers	Right Atrium	heart
47	chr3:49537000-49539600	Enhancers	Placenta	Placenta
48	chr3:49537800-49539400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr3:49537800-49539600	Enhancers	Colon Smooth Muscle	Colon
50	chr3:49538000-49548000	Weak transcription	Lung	lung

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