Variant report

Variant	rs1171833
Chromosome Location	chr10:61668567-61668568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr10:61667378-61668623	K562	blood:	n/a	chr10:61667781-61667794
2	MAX	chr10:61668180-61668613	K562	blood:	n/a	n/a
3	SP1	chr10:61668055-61668635	A549	lung:	n/a	n/a
4	POLR2A	chr10:61667976-61668598	HUVEC	blood vessel:	n/a	n/a
5	MYC	chr10:61667748-61668567	NB4	blood:	n/a	n/a
6	TEAD4	chr10:61667604-61668600	ECC-1	luminal epithelium:	n/a	n/a
7	MAFK	chr10:61667856-61668733	H1-hESC	embryonic stem cell:	n/a	chr10:61668473-61668488
8	GTF2F1	chr10:61667743-61668805	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOS	chr10:61667574-61668650	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr10:61667358-61668585	K562	blood:	n/a	n/a
11	KAP1	chr10:61667716-61668751	HEK293	kidney:	n/a	n/a
12	POLR2A	chr10:61667666-61668570	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr10:61667861-61668721	PFSK-1	brain:	n/a	n/a
14	TAF1	chr10:61667990-61668622	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPB	chr10:61667626-61668586	Hela-S3	cervix:	n/a	n/a
16	TEAD4	chr10:61668039-61668616	ECC-1	luminal epithelium:	n/a	n/a
17	ZNF384	chr10:61667588-61668690	K562	blood:	n/a	n/a
18	EP300	chr10:61668117-61668667	GM12878	blood:	n/a	n/a
19	CBX3	chr10:61667899-61668731	HCT-116	colon:	n/a	chr10:61668585-61668596
20	TEAD4	chr10:61667679-61668641	H1-hESC	embryonic stem cell:	n/a	n/a
21	IRF1	chr10:61666168-61668942	K562	blood:	n/a	chr10:61667506-61667517 chr10:61667505-61667519 chr10:61667497-61667517 chr10:61667505-61667516 chr10:61667503-61667516 chr10:61667129-61667149 chr10:61667482-61667492 chr10:61668056-61668076 chr10:61668006-61668013 chr10:61666670-61666683 chr10:61667505-61667515 chr10:61666669-61666683 chr10:61667503-61667516 chr10:61667504-61667518 chr10:61667481-61667493 chr10:61667301-61667315 chr10:61667503-61667517 chr10:61667502-61667519 chr10:61666671-61666685 chr10:61667041-61667055 chr10:61667504-61667521 chr10:61667501-61667515 chr10:61667504-61667516 chr10:61667502-61667516 chr10:61667503-61667516
22	EP300	chr10:61667399-61668666	K562	blood:	n/a	chr10:61667552-61667560
23	BRCA1	chr10:61667494-61668724	Hela-S3	cervix:	n/a	chr10:61667604-61667611
24	ZNF143	chr10:61667607-61668812	K562	blood:	n/a	chr10:61668498-61668507
25	SIN3AK20	chr10:61668032-61668680	HCT-116	colon:	n/a	n/a
26	RCOR1	chr10:61668124-61668788	K562	blood:	n/a	n/a
27	SP1	chr10:61667955-61668683	H1-hESC	embryonic stem cell:	n/a	n/a
28	EP300	chr10:61668225-61668705	H1-hESC	embryonic stem cell:	n/a	n/a
29	UBTF	chr10:61667730-61668570	K562	blood:	n/a	n/a
30	CHD2	chr10:61667620-61668759	H1-hESC	embryonic stem cell:	n/a	n/a
31	SP1	chr10:61667604-61669013	HCT-116	colon:	n/a	n/a
32	PML	chr10:61667807-61668593	K562	blood:	n/a	n/a
33	POLR2A	chr10:61667365-61668671	K562	blood:	n/a	n/a
34	FOS	chr10:61668329-61668612	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr10:61667600-61668805	PBDE	blood:	n/a	n/a
36	TBL1XR1	chr10:61667785-61668779	K562	blood:	n/a	n/a
37	PML	chr10:61667536-61668574	GM12878	blood:	n/a	n/a
38	POLR2A	chr10:61664051-61668605	GM12891	blood:	n/a	n/a
39	MAX	chr10:61667936-61668737	HCT-116	colon:	n/a	n/a
40	KAP1	chr10:61667710-61668676	U2OS	brain:	n/a	n/a
41	POLR2A	chr10:61668038-61668577	K562	blood:	n/a	n/a
42	JUND	chr10:61667458-61668611	T-47D	breast:	n/a	n/a
43	ARID3A	chr10:61667540-61668663	K562	blood:	n/a	n/a
44	TBP	chr10:61666172-61668829	Hela-S3	cervix:	n/a	n/a
45	ATF2	chr10:61667534-61668628	H1-hESC	embryonic stem cell:	n/a	n/a
46	SIN3A	chr10:61667697-61668685	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr10:61667608-61668629	Hela-S3	cervix:	n/a	n/a
48	MAX	chr10:61667917-61668650	ECC-1	luminal epithelium:	n/a	n/a
49	MAZ	chr10:61667636-61668590	IMR90	lung:	n/a	n/a
50	SIN3AK20	chr10:61668028-61668611	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:61667263..61669054-chr10:61680028..61682493,2	MCF-7	breast:
2	chr10:61666623..61668608-chr10:61670476..61672736,2	MCF-7	breast:
3	chr10:61667421..61670860-chr10:61671929..61674509,5	K562	blood:
4	chr10:61667520..61669749-chr10:61807482..61809424,2	MCF-7	breast:
5	chr10:61666876..61669628-chr10:61791272..61793178,2	MCF-7	breast:
6	chr10:61632812..61634893-chr10:61666626..61669207,2	K562	blood:
7	chr10:61666545..61669325-chr10:61676846..61678686,2	MCF-7	breast:

Variant related genes	Relation type
CCDC6	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1171820	0.81[GIH][hapmap]
rs11817261	0.80[AMR][1000 genomes]
rs11819256	0.80[AMR][1000 genomes]
rs1183347	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1184089	0.81[GIH][hapmap]
rs12572828	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12573055	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12763583	0.85[ASN][1000 genomes]
rs12776024	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1624715	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1664254	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1664257	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1664258	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs1664260	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs1664262	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs1664276	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs1664278	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1664279	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1664280	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1664281	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1684898	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1684900	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1684902	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1684904	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1684914	0.85[JPT][hapmap]
rs1684916	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17793021	0.80[AMR][1000 genomes]
rs1972950	0.92[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2166270	0.85[ASN][1000 genomes]
rs2166271	0.85[ASN][1000 genomes]
rs2440906	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2440910	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs2440916	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2440918	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450462	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450463	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450464	0.84[EUR][1000 genomes]
rs2450468	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs3763743	0.80[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3763745	0.80[CEU][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3793866	0.80[AMR][1000 genomes]
rs56221953	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61845881	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61845882	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61845883	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61845885	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs895243	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795420	chr10:61637271-61669227	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	esv1800316	chr10:61639599-61700473	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1171833	SLC16A9	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61664200-61668800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr10:61664600-61668800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr10:61664800-61668600	Active TSS	Right Atrium	heart
4	chr10:61664800-61668800	Active TSS	Stomach Smooth Muscle	stomach
5	chr10:61665000-61668600	Active TSS	Fetal Stomach	stomach
6	chr10:61665000-61668800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr10:61665200-61668800	Active TSS	Brain Angular Gyrus	brain
8	chr10:61665200-61668800	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr10:61665400-61668600	Active TSS	Colonic Mucosa	Colon
10	chr10:61665400-61668600	Active TSS	GM12878-XiMat	blood
11	chr10:61665400-61668800	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr10:61665800-61668600	Active TSS	Brain Germinal Matrix	brain
13	chr10:61666600-61668600	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr10:61666600-61668600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr10:61666600-61668600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:61666600-61668600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:61666600-61668600	Flanking Active TSS	Liver	Liver
18	chr10:61666600-61668800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:61666600-61668800	Flanking Active TSS	HUVEC	blood vessel
20	chr10:61666600-61669000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:61666800-61668600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:61666800-61668600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:61666800-61668600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr10:61666800-61668600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr10:61666800-61668600	Flanking Active TSS	Dnd41	blood
26	chr10:61666800-61668600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr10:61666800-61668600	Flanking Active TSS	NH-A	brain
28	chr10:61666800-61668600	Flanking Active TSS	NHEK	skin
29	chr10:61666800-61668800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr10:61666800-61668800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr10:61667000-61668600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr10:61667000-61668600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:61667000-61668600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr10:61667000-61668600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:61667000-61668800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr10:61667000-61668800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr10:61667000-61669000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:61667200-61668600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr10:61667400-61668600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:61667400-61668600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:61667400-61668800	Active TSS	Brain Anterior Caudate	brain
42	chr10:61667400-61668800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr10:61667600-61668600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr10:61667600-61668600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr10:61667600-61668600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:61667600-61668800	Active TSS	Brain Cingulate Gyrus	brain
47	chr10:61667600-61668800	Active TSS	NHDF-Ad	bronchial
48	chr10:61667800-61668600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr10:61667800-61668600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr10:61667800-61668600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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