Variant report

Variant	rs7602784
Chromosome Location	chr2:9849397-9849398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9695100..9696619-chr2:9848025..9849629,2	K562	blood:
2	chr2:9847027..9849818-chr2:9850088..9852900,2	K562	blood:
3	chr2:9843482..9849818-chr2:9850036..9855209,6	K562	blood:
4	chr2:9769741..9772155-chr2:9846974..9850798,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134308	Chromatin interaction
ENSG00000151694	Chromatin interaction
ENSG00000271855	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10164660	0.83[ASN][1000 genomes]
rs10178017	0.90[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10200779	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10202938	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10929596	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10929597	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10929598	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10929600	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10929602	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10929605	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1123269	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs11674642	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11680429	0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11685771	0.82[MEX][hapmap]
rs11695437	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11892176	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11901380	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11902412	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11902608	0.82[ASN][1000 genomes]
rs12466594	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12472594	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12475853	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs12476232	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs12991432	0.83[ASN][1000 genomes]
rs12993968	0.82[ASN][1000 genomes]
rs13024852	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13028425	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs13395171	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs13398163	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs13398193	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs13398304	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1877949	0.82[ASN][1000 genomes]
rs1877950	0.83[ASN][1000 genomes]
rs1877951	0.83[ASN][1000 genomes]
rs1877953	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2357263	0.95[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357264	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2357265	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4459704	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4507070	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4668636	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4668637	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4668638	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4668639	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4668640	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4668641	0.80[ASN][1000 genomes]
rs4668642	0.83[ASN][1000 genomes]
rs4668643	0.83[ASN][1000 genomes]
rs4669427	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669428	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669429	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669430	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669432	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4669433	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4669435	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4669437	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4669441	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4669445	0.86[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs4669446	0.83[ASN][1000 genomes]
rs5020306	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58961346	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6432033	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6724483	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727688	0.83[ASN][1000 genomes]
rs6735280	0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6736421	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6738072	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6752842	0.84[ASN][1000 genomes]
rs6756567	0.86[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7423455	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7578933	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7592044	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885572	0.83[EUR][1000 genomes];0.90[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	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7602784	HPCAL1	cis	parietal	SCAN
rs7602784	ODC1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9837000-9849600	Weak transcription	Pancreas	Pancrea
2	chr2:9843800-9852000	Weak transcription	Left Ventricle	heart
3	chr2:9844200-9852000	Weak transcription	Esophagus	oesophagus
4	chr2:9844400-9849600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:9844400-9849600	Weak transcription	HMEC	breast
6	chr2:9844600-9849800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:9845000-9849600	Weak transcription	Spleen	Spleen
8	chr2:9845000-9850000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:9845200-9849800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:9845200-9852000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:9845400-9860600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:9845600-9851600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:9846800-9854800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:9848000-9849400	Enhancers	K562	blood
15	chr2:9848000-9850600	Enhancers	GM12878-XiMat	blood
16	chr2:9848000-9852400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr2:9848200-9852200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:9848400-9850600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:9848400-9851200	Weak transcription	Right Ventricle	heart
20	chr2:9848400-9852400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:9848800-9849400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:9848800-9850200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:9849000-9849800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:9849000-9852400	Enhancers	Primary T helper cells PMA-I stimulated	--

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