Variant report

Variant	rs2860490
Chromosome Location	chr10:52327487-52327488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52324915..52329170-chr10:52335171..52340296,4	K562	blood:
2	chr10:52324915..52329170-chr10:52337236..52340296,3	K562	blood:
3	chr10:52319893..52329540-chr10:52377624..52388129,20	MCF-7	breast:
4	chr10:52323633..52328946-chr10:52382781..52388541,7	K562	blood:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1203383	0.85[TSI][hapmap]
rs1203391	0.85[TSI][hapmap]
rs1203427	0.85[TSI][hapmap]
rs13376734	0.84[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2208035	0.93[YRI][hapmap]
rs2208037	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339508	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339509	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983348	1.00[ASW][hapmap];0.87[LWK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs2983352	1.00[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983358	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983362	1.00[ASW][hapmap];0.93[CEU][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983365	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983372	0.93[YRI][hapmap]
rs3001853	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs3001855	0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs3001856	0.82[EUR][1000 genomes]
rs3001865	0.84[CEU][hapmap]
rs3001884	0.84[EUR][1000 genomes]
rs3011708	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	0.86[YRI][hapmap]
rs3011778	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011781	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011799	0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56153288	0.83[EUR][1000 genomes]
rs56266445	0.83[EUR][1000 genomes]
rs57025029	0.86[EUR][1000 genomes]
rs67094247	0.84[EUR][1000 genomes]
rs7067608	0.83[EUR][1000 genomes]
rs7074349	0.84[EUR][1000 genomes]
rs7077555	0.84[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7078586	0.83[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs7094723	0.91[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096920	0.84[EUR][1000 genomes]
rs72803755	0.85[EUR][1000 genomes]
rs7897345	0.84[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7904446	0.84[EUR][1000 genomes]
rs7908093	0.87[EUR][1000 genomes]
rs910819	0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2860490	C20orf103	trans	lymphoblastoid	seeQTL
rs2860490	CSTF2T	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52305400-52329600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr10:52306000-52331800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr10:52308000-52337200	Weak transcription	Primary T cells from cord blood	blood
5	chr10:52311000-52335800	Weak transcription	Esophagus	oesophagus
6	chr10:52312800-52335800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:52312800-52335800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr10:52313200-52333200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr10:52313600-52337400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr10:52315000-52329600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:52315200-52337400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr10:52315600-52336000	Weak transcription	GM12878-XiMat	blood
13	chr10:52316400-52331800	Weak transcription	Lung	lung
14	chr10:52316800-52332000	Weak transcription	Aorta	Aorta
15	chr10:52316800-52332600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr10:52318200-52331800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr10:52318400-52329600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr10:52319200-52335800	Weak transcription	Spleen	Spleen
19	chr10:52319600-52335600	Weak transcription	NHEK	skin
20	chr10:52321600-52335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:52321800-52331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:52321800-52331600	Weak transcription	Psoas Muscle	Psoas
23	chr10:52321800-52335600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:52321800-52335600	Weak transcription	Adipose Nuclei	Adipose
25	chr10:52322000-52330200	Weak transcription	Hela-S3	cervix
26	chr10:52322000-52331000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr10:52322000-52335800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:52322000-52337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr10:52322000-52348600	Weak transcription	Fetal Stomach	stomach
30	chr10:52322200-52335600	Weak transcription	NHLF	lung
31	chr10:52322800-52333800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:52322800-52335600	Weak transcription	Fetal Lung	lung
33	chr10:52322800-52336000	Weak transcription	Placenta	Placenta
34	chr10:52323600-52327800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr10:52323800-52328200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr10:52324000-52329200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr10:52324000-52331800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:52324000-52336600	Weak transcription	Thymus	Thymus
39	chr10:52324000-52337400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr10:52324200-52329600	Weak transcription	Fetal Intestine Large	intestine
41	chr10:52324400-52330400	Weak transcription	Fetal Intestine Small	intestine
42	chr10:52324400-52331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr10:52324400-52336800	Weak transcription	Primary B cells from cord blood	blood
44	chr10:52324400-52336800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr10:52325200-52328200	Enhancers	Brain Hippocampus Middle	brain
46	chr10:52325200-52328200	Enhancers	Brain Substantia Nigra	brain
47	chr10:52325400-52336000	Weak transcription	Stomach Mucosa	stomach
48	chr10:52325600-52328400	Enhancers	Brain Anterior Caudate	brain
49	chr10:52325600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:52325800-52331000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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