Variant report

Variant	rs1913621
Chromosome Location	chr2:99362400-99362401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99361547..99363646-chr2:99366990..99369948,2	MCF-7	breast:
2	chr2:99346209..99349698-chr2:99359488..99362618,3	MCF-7	breast:
3	chr2:99356397..99359071-chr2:99359903..99362484,2	K562	blood:
4	chr2:99360967..99363379-chr2:99408314..99410102,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1016124	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10173832	0.83[ASN][1000 genomes]
rs10177696	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10194177	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10199267	0.81[EUR][1000 genomes]
rs10200288	0.95[ASN][1000 genomes]
rs10210711	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10460485	0.81[EUR][1000 genomes]
rs10496332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123747	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123749	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123751	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11885883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471383	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12477450	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12615301	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622931	0.81[EUR][1000 genomes]
rs12993424	0.96[ASN][1000 genomes]
rs13391483	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391794	0.81[EUR][1000 genomes]
rs13410406	0.81[EUR][1000 genomes]
rs1514916	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1517681	0.96[ASN][1000 genomes]
rs2013983	0.96[ASN][1000 genomes]
rs28783173	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34521960	0.96[ASN][1000 genomes]
rs35477458	0.96[ASN][1000 genomes]
rs41445250	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851150	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851153	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4851154	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58666702	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60024860	0.81[EUR][1000 genomes]
rs6712597	0.80[ASN][1000 genomes]
rs6733957	0.81[EUR][1000 genomes]
rs6737760	0.81[EUR][1000 genomes]
rs6740656	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7420869	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7577636	0.81[EUR][1000 genomes]
rs7581128	0.81[CHB][hapmap]
rs7599792	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs885036	0.81[CHB][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv1002315	chr2:99361475-99368975	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1913621	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99348400-99367000	Weak transcription	Esophagus	oesophagus
2	chr2:99354600-99364600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr2:99354800-99364000	Weak transcription	Dnd41	blood
4	chr2:99359200-99362400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:99359200-99362400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:99359200-99362600	Enhancers	Primary T cells fromperipheralblood	blood
7	chr2:99359200-99362600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr2:99359200-99362800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:99359200-99363000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:99359400-99362400	Enhancers	Primary T cells from cord blood	blood
11	chr2:99359400-99362400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:99359400-99362400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr2:99359600-99364200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:99359600-99364400	Weak transcription	Placenta	Placenta
15	chr2:99359600-99364400	Weak transcription	Spleen	Spleen
16	chr2:99359600-99367200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:99359600-99374000	Weak transcription	Aorta	Aorta
18	chr2:99360000-99362400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr2:99360400-99362600	Enhancers	Fetal Heart	heart
20	chr2:99361200-99364200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:99361200-99364200	Weak transcription	Fetal Thymus	thymus
22	chr2:99361200-99365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:99361400-99363800	Weak transcription	Adipose Nuclei	Adipose
24	chr2:99361400-99364400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:99361400-99364400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:99361400-99364400	Weak transcription	HMEC	breast
27	chr2:99361400-99365400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:99361400-99365600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:99361400-99374000	Weak transcription	Pancreas	Pancrea
30	chr2:99361600-99364400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:99362000-99362400	Weak transcription	HepG2	liver
32	chr2:99362200-99362400	Enhancers	Right Ventricle	heart
33	chr2:99362200-99362400	Enhancers	Thymus	Thymus
34	chr2:99362200-99362600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:99362200-99364200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:99362400-99364000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:99362400-99364000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:99362400-99364000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:99362400-99364200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:99362400-99365200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:99362400-99372800	Weak transcription	Primary T cells from cord blood	blood

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