Variant report

Variant	rs12477450
Chromosome Location	chr2:99340684-99340685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99338843..99341034-chr2:99341737..99344169,2	MCF-7	breast:
2	chr2:99316162..99318899-chr2:99339583..99342162,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1016124	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10173832	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10177696	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10194177	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10199267	0.88[EUR][1000 genomes]
rs10210711	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10460485	0.88[EUR][1000 genomes]
rs10496332	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11123747	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11123749	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11123751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11885883	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12471383	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12615301	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12622931	0.88[EUR][1000 genomes]
rs13391483	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13391794	0.88[EUR][1000 genomes]
rs13410406	0.88[EUR][1000 genomes]
rs13428808	0.87[EUR][1000 genomes]
rs1514916	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1913621	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]
rs28783173	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41445250	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]
rs4851150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851153	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4851154	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5008045	0.82[EUR][1000 genomes]
rs58666702	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[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	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7420869	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7558236	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7577636	0.83[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs7599792	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7601040	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv2841	chr2:99296874-99342362	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv535836	chr2:99329084-99353519	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	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
rs12477450	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99326400-99342600	Weak transcription	Adipose Nuclei	Adipose
2	chr2:99326400-99343600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:99326400-99346400	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:99326800-99342600	Weak transcription	Liver	Liver
5	chr2:99326800-99343800	Weak transcription	Small Intestine	intestine
6	chr2:99333000-99342800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:99334200-99343200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:99335200-99343600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:99335200-99346600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:99335400-99342800	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:99335400-99343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:99335600-99343200	Strong transcription	Fetal Thymus	thymus
13	chr2:99335600-99345800	Weak transcription	Right Ventricle	heart
14	chr2:99336600-99342200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:99337000-99342600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:99337000-99344400	Weak transcription	Fetal Stomach	stomach
17	chr2:99337000-99346200	Weak transcription	Aorta	Aorta
18	chr2:99337200-99342400	Weak transcription	Fetal Brain Female	brain
19	chr2:99337200-99343200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:99337200-99344000	Weak transcription	Spleen	Spleen
21	chr2:99337600-99340800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr2:99337600-99341600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:99337600-99342600	Weak transcription	Colonic Mucosa	Colon
24	chr2:99337600-99342800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:99337800-99341800	Weak transcription	Fetal Kidney	kidney
26	chr2:99338000-99346200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:99338200-99341600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:99338200-99346200	Weak transcription	Placenta	Placenta
29	chr2:99338400-99342200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:99338800-99342200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:99338800-99343600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:99339000-99343000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:99339000-99343600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:99339000-99345800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:99339200-99341200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:99339600-99341200	Genic enhancers	Primary T cells from cord blood	blood
37	chr2:99339600-99341200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr2:99339600-99341200	Strong transcription	HepG2	liver
39	chr2:99339600-99341800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:99339800-99341200	Strong transcription	HUVEC	blood vessel
41	chr2:99339800-99342200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:99339800-99342600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:99340000-99342600	Enhancers	Brain Angular Gyrus	brain
44	chr2:99340000-99345800	Weak transcription	Primary B cells from cord blood	blood
45	chr2:99340000-99345800	Weak transcription	Right Atrium	heart
46	chr2:99340200-99341200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:99340200-99341400	Strong transcription	Dnd41	blood
48	chr2:99340200-99341800	Weak transcription	Fetal Intestine Large	intestine
49	chr2:99340200-99342200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:99340200-99342200	Weak transcription	Fetal Intestine Small	intestine

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