Variant report

Variant	rs1800975
Chromosome Location	chr9:100459578-100459579
allele	A/G
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	JUND	chr9:100458945-100459914	K562	blood:	n/a	chr9:100459358-100459367
2	POLR2A	chr9:100459489-100460021	HepG2	liver:	n/a	n/a
3	YY1	chr9:100459500-100459649	K562	blood:	n/a	n/a
4	RCOR1	chr9:100458712-100459877	K562	blood:	n/a	n/a
5	HEY1	chr9:100459248-100459974	HepG2	liver:	n/a	n/a
6	POLR2A	chr9:100459214-100459964	MCF-7	breast:	n/a	n/a
7	POLR2A	chr9:100459372-100459947	GM12891	blood:	n/a	n/a
8	PAX5	chr9:100459217-100459705	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:100459311-100460046	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr9:100458110-100460285	MCF10A-Er-Src	breast:	n/a	n/a
11	CTBP2	chr9:100459035-100459798	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr9:100459137-100459960	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr9:100459224-100459943	A549	lung:	n/a	n/a
14	ELK1	chr9:100459511-100459787	K562	blood:	n/a	n/a
15	EP300	chr9:100459246-100459808	GM12878	blood:	n/a	chr9:100459730-100459746
16	TAF1	chr9:100459187-100459760	H1-hESC	embryonic stem cell:	n/a	n/a
17	HMGN3	chr9:100459072-100459826	K562	blood:	n/a	n/a
18	POLR2A	chr9:100459015-100459940	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr9:100459568-100459748	K562	blood:	n/a	chr9:100459730-100459740
20	POU2F2	chr9:100459437-100459624	GM12878	blood:	n/a	n/a
21	TAF1	chr9:100459207-100459918	GM12878	blood:	n/a	n/a
22	YY1	chr9:100459039-100459749	A549	lung:	n/a	chr9:100459098-100459112
23	YY1	chr9:100459179-100459892	GM12878	blood:	n/a	n/a
24	RFX5	chr9:100459393-100459791	GM12878	blood:	n/a	n/a
25	ZNF263	chr9:100458787-100459805	HEK293-T-REx	kidney:	n/a	n/a
26	CTCF	chr9:100459577-100459729	Spleen_OC	spleen:	n/a	n/a
27	NR3C1	chr9:100459504-100459919	A549	lung:	n/a	n/a
28	YY1	chr9:100459382-100459753	K562	blood:	n/a	n/a
29	POLR2A	chr9:100459256-100459896	HUVEC	blood vessel:	n/a	n/a
30	MXI1	chr9:100458379-100460052	GM12878	blood:	n/a	n/a
31	MXI1	chr9:100458476-100460001	Hela-S3	cervix:	n/a	n/a
32	TBP	chr9:100459334-100460093	GM12878	blood:	n/a	n/a
33	MAX	chr9:100458982-100459954	GM12878	blood:	n/a	n/a
34	NRF1	chr9:100459422-100459912	GM12878	blood:	n/a	chr9:100459609-100459620 chr9:100459691-100459705 chr9:100459609-100459623 chr9:100459606-100459620 chr9:100459696-100459705 chr9:100459694-100459705 chr9:100459694-100459708 chr9:100459694-100459705
35	POLR2A	chr9:100459301-100460008	GM12878	blood:	n/a	n/a
36	SIN3AK20	chr9:100458965-100459819	SK-N-SH	brain:	n/a	n/a
37	MAX	chr9:100459043-100459891	K562	blood:	n/a	n/a
38	POLR2A	chr9:100459048-100459978	GM19193	blood:	n/a	n/a
39	ELK1	chr9:100459206-100459899	GM12878	blood:	n/a	n/a
40	MAZ	chr9:100458852-100460181	GM12878	blood:	n/a	n/a
41	GTF2B	chr9:100459414-100459722	K562	blood:	n/a	n/a
42	MYC	chr9:100458449-100460078	K562	blood:	n/a	n/a
43	POLR2A	chr9:100459033-100459949	Hela-S3	cervix:	n/a	n/a
44	HCFC1	chr9:100458902-100459928	K562	blood:	n/a	n/a
45	YY1	chr9:100459219-100459776	K562	blood:	n/a	n/a
46	TCF7L2	chr9:100459037-100459827	Hela-S3	cervix:	n/a	n/a
47	NFYB	chr9:100459541-100459888	GM12878	blood:	n/a	n/a
48	ARID3A	chr9:100459519-100460282	HepG2	liver:	n/a	n/a
49	POLR2A	chr9:100459147-100460335	HepG2	liver:	n/a	n/a
50	MAX	chr9:100459187-100459926	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:100457791..100462084-chr9:100462112..100466505,5	K562	blood:
2	chr9:100458137..100459680-chr9:100684005..100686050,2	MCF-7	breast:
3	chr6:111195721..111196526-chr9:100459272..100459831,2	Hela-S3	cervix:
4	chr9:100393846..100397319-chr9:100457855..100461087,4	MCF-7	breast:
5	chr9:100393858..100397326-chr9:100457081..100460285,5	MCF-7	breast:
6	chr6:144164140..144164989-chr9:100459477..100460017,2	HCT-116	colon:
7	chr9:100458946..100460891-chr9:100746178..100747740,2	MCF-7	breast:

Variant related genes	Relation type
KRT18P13	TF binding region
ENSG00000266608	TF binding region
XPA	TF binding region
ENSG00000136938	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000136925	Chromatin interaction
ENSG00000136937	Chromatin interaction
ENSG00000123505	Chromatin interaction
ENSG00000135521	Chromatin interaction
ENSG00000266608	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10983030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10983447	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12379552	0.84[EUR][1000 genomes]
rs2026132	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2036959	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2668792	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2668793	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2668798	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2773347	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2773351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2805767	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2805775	0.88[EUR][1000 genomes]
rs2805777	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2805779	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2805824	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2805825	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2805826	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2805828	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2805829	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2805832	0.82[ASW][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2805837	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2805839	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2805840	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2808668	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808673	1.00[CEU][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2808675	1.00[CEU][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2808677	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2808683	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2808685	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2808686	0.92[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2808687	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2808689	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2808691	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2808692	0.90[EUR][1000 genomes]
rs2808701	0.88[EUR][1000 genomes]
rs2808703	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478325	0.88[EUR][1000 genomes]
rs7853179	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs958346	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]

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	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1800975	XPA	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100457800-100459800	Active TSS	NHLF	lung
2	chr9:100457800-100460000	Active TSS	Aorta	Aorta
3	chr9:100458000-100459600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:100458000-100459800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:100458000-100460000	Active TSS	Ovary	ovary
6	chr9:100458200-100460000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:100458200-100460000	Active TSS	Fetal Muscle Trunk	muscle
8	chr9:100458200-100460000	Active TSS	Pancreas	Pancrea
9	chr9:100458400-100459600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:100458400-100459800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:100458400-100459800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr9:100458400-100459800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:100458400-100459800	Active TSS	Hela-S3	cervix
14	chr9:100458400-100459800	Active TSS	HSMM	muscle
15	chr9:100458400-100459800	Active TSS	NHDF-Ad	bronchial
16	chr9:100458400-100460000	Active TSS	Esophagus	oesophagus
17	chr9:100458400-100460000	Active TSS	Left Ventricle	heart
18	chr9:100458400-100460200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:100458400-100460200	Active TSS	Psoas Muscle	Psoas
20	chr9:100458400-100460400	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr9:100458600-100459600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:100458600-100459600	Active TSS	Gastric	stomach
23	chr9:100458600-100459800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:100458600-100459800	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr9:100458600-100459800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:100458600-100459800	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr9:100458600-100459800	Active TSS	Colon Smooth Muscle	Colon
28	chr9:100458600-100459800	Active TSS	Fetal Intestine Large	intestine
29	chr9:100458600-100459800	Active TSS	Fetal Intestine Small	intestine
30	chr9:100458600-100459800	Active TSS	Fetal Muscle Leg	muscle
31	chr9:100458600-100459800	Active TSS	Fetal Stomach	stomach
32	chr9:100458600-100459800	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr9:100458600-100459800	Active TSS	Small Intestine	intestine
34	chr9:100458600-100459800	Active TSS	Stomach Smooth Muscle	stomach
35	chr9:100458600-100459800	Active TSS	Thymus	Thymus
36	chr9:100458600-100459800	Active TSS	GM12878-XiMat	blood
37	chr9:100458600-100459800	Active TSS	K562	blood
38	chr9:100458600-100459800	Active TSS	Osteobl	bone
39	chr9:100458600-100460000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:100458600-100460000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:100458600-100460000	Active TSS	Brain Anterior Caudate	brain
42	chr9:100458600-100460000	Active TSS	Colonic Mucosa	Colon
43	chr9:100458600-100460000	Active TSS	Fetal Brain Female	brain
44	chr9:100458600-100460000	Active TSS	Placenta	Placenta
45	chr9:100458600-100460000	Active TSS	Right Ventricle	heart
46	chr9:100458600-100460200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr9:100458800-100459600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:100458800-100459600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr9:100458800-100459800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr9:100458800-100459800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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