Variant report

Variant	rs10960810
Chromosome Location	chr9:12817881-12817882
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	SP1	chr9:12817499-12818283	A549	lung:	n/a	n/a
2	FOXA2	chr9:12817726-12818089	HepG2	liver:	n/a	n/a
3	NR3C1	chr9:12817576-12818098	A549	lung:	n/a	chr9:12818045-12818062 chr9:12817901-12817915 chr9:12817998-12818011 chr9:12817900-12817915
4	POLR2A	chr9:12817875-12817923	MCF-7	breast:	n/a	n/a
5	FOS	chr9:12817614-12817977	MCF10A-Er-Src	breast:	n/a	chr9:12817733-12817745
6	JUND	chr9:12817700-12818109	A549	lung:	n/a	chr9:12817733-12817745
7	GATA3	chr9:12817641-12818125	A549	lung:	n/a	n/a
8	POLR2A	chr9:12817306-12818024	HepG2	liver:	n/a	n/a
9	SIN3AK20	chr9:12817533-12818364	MCF-7	breast:	n/a	n/a
10	POLR2A	chr9:12817780-12818034	A549	lung:	n/a	n/a
11	JUND	chr9:12817656-12817967	HepG2	liver:	n/a	chr9:12817733-12817745
12	POLR2A	chr9:12817836-12817903	HepG2	liver:	n/a	n/a
13	FOXA1	chr9:12817712-12818169	HepG2	liver:	n/a	n/a
14	POLR2A	chr9:12817731-12818086	HepG2	liver:	n/a	n/a
15	POLR2A	chr9:12817036-12818541	MCF10A-Er-Src	breast:	n/a	n/a
16	FOXA1	chr9:12817706-12818268	HepG2	liver:	n/a	n/a
17	MAFF	chr9:12817791-12817939	HepG2	liver:	n/a	n/a
18	FOXA1	chr9:12817805-12818120	T-47D	breast:	n/a	n/a
19	FOXA1	chr9:12817825-12818108	T-47D	breast:	n/a	n/a
20	MYC	chr9:12817729-12817929	MCF10A-Er-Src	breast:	n/a	n/a
21	EBF1	chr9:12817765-12818160	GM12878	blood:	n/a	n/a
22	TBP	chr9:12817792-12817992	HepG2	liver:	n/a	n/a
23	GATA3	chr9:12816601-12818747	A549	lung:	n/a	chr9:12816841-12816851 chr9:12816849-12816859
24	SP1	chr9:12817472-12818206	HCT-116	colon:	n/a	n/a
25	NR3C1	chr9:12817772-12818019	A549	lung:	n/a	chr9:12817901-12817915 chr9:12817998-12818011 chr9:12817900-12817915
26	MAX	chr9:12817626-12818250	A549	lung:	n/a	n/a
27	TCF12	chr9:12816580-12818356	A549	lung:	n/a	chr9:12816975-12816984
28	POLR2A	chr9:12817721-12817921	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr9:12817614-12817951	MCF10A-Er-Src	breast:	n/a	chr9:12817733-12817745
30	EP300	chr9:12817494-12818315	A549	lung:	n/a	chr9:12817983-12817993
31	ZNF217	chr9:12817726-12818071	MCF-7	breast:	n/a	n/a
32	MAX	chr9:12817691-12818203	A549	lung:	n/a	n/a
33	USF1	chr9:12817674-12818190	A549	lung:	n/a	chr9:12817883-12817899
34	GATA3	chr9:12817688-12818101	MCF-7	breast:	n/a	n/a
35	FOXA2	chr9:12817709-12818197	A549	lung:	n/a	n/a
36	FOXA1	chr9:12817638-12818258	A549	lung:	n/a	n/a
37	EP300	chr9:12817430-12818323	A549	lung:	n/a	chr9:12817983-12817993
38	ARID3A	chr9:12816761-12818215	HepG2	liver:	n/a	chr9:12817708-12817724
39	FOXA1	chr9:12817674-12818272	HepG2	liver:	n/a	n/a
40	POLR2A	chr9:12817608-12818053	HCT-116	colon:	n/a	n/a
41	NR3C1	chr9:12817691-12818160	A549	lung:	n/a	chr9:12818045-12818062 chr9:12817901-12817915 chr9:12817998-12818011 chr9:12817900-12817915
42	NR3C1	chr9:12817677-12818217	A549	lung:	n/a	chr9:12818045-12818062 chr9:12817901-12817915 chr9:12817998-12818011 chr9:12817900-12817915
43	FOXA1	chr9:12817562-12818236	A549	lung:	n/a	n/a
44	NR3C1	chr9:12817615-12818242	A549	lung:	n/a	chr9:12818045-12818062 chr9:12817901-12817915 chr9:12817998-12818011 chr9:12817900-12817915
45	NR3C1	chr9:12817590-12818162	A549	lung:	n/a	chr9:12818045-12818062 chr9:12817901-12817915 chr9:12817998-12818011 chr9:12817900-12817915
46	GATA3	chr9:12817577-12818242	MCF-7	breast:	n/a	n/a
47	POLR2A	chr9:12817778-12817983	A549	lung:	n/a	n/a
48	FOXA2	chr9:12817664-12818262	A549	lung:	n/a	n/a
49	JUND	chr9:12817697-12818163	A549	lung:	n/a	chr9:12817733-12817745
50	CHD2	chr9:12817721-12817972	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:12810284..12814602-chr9:12816113..12819154,5	MCF-7	breast:
2	chr9:12817203..12820022-chr9:12879979..12881998,2	MCF-7	breast:
3	chr9:12816711..12819917-chr9:12821131..12823680,3	MCF-7	breast:
4	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
5	chr9:12815854..12818984-chr9:12830927..12834079,3	MCF-7	breast:
6	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:
7	chr9:12816957..12819670-chr9:12821766..12823551,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235448	TF binding region
ENSG00000153714	Chromatin interaction
ENSG00000235448	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10809847	0.93[EUR][1000 genomes]
rs10960809	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10960811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16929629	0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs35991181	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4111024	0.89[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6474734	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6474735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6474736	0.82[CHB][hapmap]
rs7049208	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7846724	0.82[CHB][hapmap]
rs7875509	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][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	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv892575	chr9:12804243-12852462	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12808600-12818400	Weak transcription	Fetal Brain Male	brain
2	chr9:12809200-12821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:12814400-12818800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:12814600-12819200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:12814600-12824800	Weak transcription	Psoas Muscle	Psoas
6	chr9:12814800-12823200	Weak transcription	Colonic Mucosa	Colon
7	chr9:12815000-12818200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:12815000-12818800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:12815000-12819200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:12815000-12819800	Enhancers	Fetal Intestine Small	intestine
11	chr9:12815200-12818200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:12815200-12818200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr9:12815200-12818200	Weak transcription	Fetal Stomach	stomach
14	chr9:12815200-12819200	Enhancers	Colon Smooth Muscle	Colon
15	chr9:12815200-12819200	Enhancers	HMEC	breast
16	chr9:12815200-12819600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:12815200-12819800	Enhancers	Fetal Intestine Large	intestine
18	chr9:12815200-12820200	Enhancers	NHLF	lung
19	chr9:12815200-12821400	Enhancers	Osteobl	bone
20	chr9:12815200-12822400	Weak transcription	Brain Angular Gyrus	brain
21	chr9:12815600-12819200	Flanking Active TSS	A549	lung
22	chr9:12815800-12819000	Weak transcription	HUVEC	blood vessel
23	chr9:12815800-12821600	Weak transcription	HSMM	muscle
24	chr9:12816200-12832000	Weak transcription	HSMMtube	muscle
25	chr9:12816400-12818400	Enhancers	Liver	Liver
26	chr9:12816600-12819600	Enhancers	Hela-S3	cervix
27	chr9:12816800-12818600	Flanking Active TSS	HepG2	liver
28	chr9:12817000-12819200	Enhancers	Fetal Lung	lung
29	chr9:12817000-12820200	Enhancers	NHDF-Ad	bronchial
30	chr9:12817200-12818000	Enhancers	Brain Hippocampus Middle	brain
31	chr9:12817200-12818000	Enhancers	NHEK	skin
32	chr9:12817200-12818600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr9:12817200-12818800	Enhancers	Pancreas	Pancrea
34	chr9:12817200-12819200	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr9:12817200-12819200	Enhancers	Small Intestine	intestine
36	chr9:12817200-12819400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:12817400-12818000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr9:12817400-12819200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:12817400-12819600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:12817400-12819800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr9:12817600-12818000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:12817600-12818000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr9:12817600-12818000	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr9:12817600-12818200	Enhancers	Gastric	stomach
45	chr9:12817600-12818400	Enhancers	Brain Substantia Nigra	brain
46	chr9:12817600-12818600	Enhancers	Brain Anterior Caudate	brain
47	chr9:12817600-12818800	Enhancers	Brain Cingulate Gyrus	brain
48	chr9:12817600-12819000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:12817600-12819400	Enhancers	Adipose Nuclei	Adipose
50	chr9:12817600-12820000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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