Variant report

Variant	rs3011711
Chromosome Location	chr10:52351333-52351334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52350545..52352167-chr10:52381808..52384561,2	K562	blood:
2	chr10:52350667..52353261-chr10:52381881..52384796,3	K562	blood:
3	chr10:52346124..52348507-chr10:52350618..52352666,3	K562	blood:
4	chr10:52351092..52355625-chr10:52355822..52361152,8	K562	blood:
5	chr10:52150758..52153271-chr10:52349900..52352192,2	K562	blood:

Variant related genes	Relation type
ENSG00000269700	Chromatin interaction
ENSG00000226200	Chromatin interaction
ENSG00000198964	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];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339508	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339509	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860490	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]
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];0.96[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983358	0.93[YRI][hapmap];0.82[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][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];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983365	0.96[AFR][1000 genomes];0.95[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	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	0.86[YRI][hapmap]
rs3011778	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011781	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011799	0.93[YRI][hapmap];0.85[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
rs3011711	C20orf103	trans	lymphoblastoid	seeQTL
rs3011711	CSTF2T	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52336800-52363000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:52337800-52352800	Weak transcription	Fetal Brain Male	brain
3	chr10:52338000-52356400	Weak transcription	Fetal Brain Female	brain
4	chr10:52338000-52363800	Weak transcription	Fetal Kidney	kidney
5	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
6	chr10:52338200-52353600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:52338200-52353800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr10:52338600-52353400	Weak transcription	Brain Germinal Matrix	brain
9	chr10:52338600-52353600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:52340400-52360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr10:52341400-52355400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:52341400-52360200	Weak transcription	GM12878-XiMat	blood
14	chr10:52341800-52351800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:52341800-52352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:52341800-52355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:52341800-52362000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr10:52342000-52352000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr10:52342200-52351800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr10:52342400-52351600	Weak transcription	Brain Angular Gyrus	brain
21	chr10:52342400-52353000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:52342600-52356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:52342800-52360200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr10:52343000-52353000	Weak transcription	Fetal Heart	heart
25	chr10:52343400-52360600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr10:52343600-52356200	Weak transcription	Stomach Mucosa	stomach
27	chr10:52343600-52362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr10:52343800-52360000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr10:52345000-52353000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:52346000-52355400	Weak transcription	Colon Smooth Muscle	Colon
31	chr10:52346400-52358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr10:52346600-52351800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:52346600-52351800	Weak transcription	Right Atrium	heart
34	chr10:52346600-52352600	Weak transcription	HSMMtube	muscle
35	chr10:52346600-52352600	Weak transcription	NHDF-Ad	bronchial
36	chr10:52346600-52352800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:52346600-52355400	Weak transcription	Psoas Muscle	Psoas
38	chr10:52346600-52363400	Weak transcription	Adipose Nuclei	Adipose
39	chr10:52346600-52363800	Weak transcription	Spleen	Spleen
40	chr10:52346800-52351400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:52346800-52352600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr10:52346800-52352800	Weak transcription	NHLF	lung
43	chr10:52346800-52353200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:52346800-52360600	Weak transcription	HUVEC	blood vessel
45	chr10:52347000-52352800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:52347000-52352800	Weak transcription	HMEC	breast
47	chr10:52347000-52353000	Weak transcription	NHEK	skin
48	chr10:52347000-52353600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr10:52347000-52359600	Weak transcription	A549	lung
50	chr10:52347200-52352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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