Variant report

Variant	rs41445250
Chromosome Location	chr2:99357165-99357166
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	chr2:99356397..99359071-chr2:99359903..99362484,2	K562	blood:
2	chr2:99344987..99348857-chr2:99353398..99358314,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1016124	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10173832	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10174321	0.84[ASN][1000 genomes]
rs10177696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10194177	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199267	0.88[EUR][1000 genomes]
rs10200288	0.89[ASN][1000 genomes]
rs10210711	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10460485	0.88[EUR][1000 genomes]
rs10496332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123747	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11123749	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11123751	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11885883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12471383	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12477450	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12615301	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12622931	0.88[EUR][1000 genomes]
rs12993424	0.91[ASN][1000 genomes]
rs13391483	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13391794	0.88[EUR][1000 genomes]
rs13392306	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13410406	0.88[EUR][1000 genomes]
rs13428808	0.87[EUR][1000 genomes]
rs1514916	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1517681	0.91[ASN][1000 genomes]
rs1913621	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]
rs2013983	0.91[ASN][1000 genomes]
rs28783173	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34521960	0.91[ASN][1000 genomes]
rs35477458	0.91[ASN][1000 genomes]
rs4851150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851153	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851154	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5008045	0.82[EUR][1000 genomes]
rs58666702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60024860	0.88[EUR][1000 genomes]
rs6706340	0.82[EUR][1000 genomes]
rs6733957	0.88[EUR][1000 genomes]
rs6737760	0.88[EUR][1000 genomes]
rs6740656	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7420869	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7577636	0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs7581128	0.81[CHB][hapmap]
rs7599792	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7601040	0.82[EUR][1000 genomes]
rs885036	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41445250	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99348400-99367000	Weak transcription	Esophagus	oesophagus
2	chr2:99348600-99359200	Weak transcription	Aorta	Aorta
3	chr2:99348800-99360600	Weak transcription	Lung	lung
4	chr2:99349200-99357200	Enhancers	HepG2	liver
5	chr2:99351800-99360400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:99351800-99360600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:99352800-99359000	Weak transcription	Placenta	Placenta
8	chr2:99352800-99360400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:99353400-99358000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:99353400-99359400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:99353400-99360400	Weak transcription	HMEC	breast
12	chr2:99353600-99359400	Weak transcription	HUVEC	blood vessel
13	chr2:99354000-99359400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:99354600-99359200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:99354600-99359600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:99354600-99364600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:99354800-99360600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:99354800-99364000	Weak transcription	Dnd41	blood
19	chr2:99355000-99359200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:99355000-99359200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:99355000-99362200	Weak transcription	Thymus	Thymus
22	chr2:99355200-99359200	Weak transcription	Gastric	stomach
23	chr2:99355200-99359400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:99355200-99360800	Weak transcription	Small Intestine	intestine
25	chr2:99355600-99359200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:99355600-99359600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:99355800-99359200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:99355800-99359200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:99355800-99359200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:99355800-99359400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:99356000-99359400	Weak transcription	Primary T cells from cord blood	blood
32	chr2:99356200-99359200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:99356600-99357400	Enhancers	Pancreas	Pancrea
34	chr2:99356600-99357600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr2:99356600-99360000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:99356800-99357600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:99356800-99357600	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr2:99357000-99357400	Enhancers	Stomach Smooth Muscle	stomach

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