Variant report

Variant	rs7072554
Chromosome Location	chr10:1090988-1090989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:1089899-1091365	MCF10A-Er-Src	breast:	n/a	n/a
2	WRNIP1	chr10:1090888-1091130	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:1088970-1092654	PBDE	blood:	n/a	n/a
4	POLR2A	chr10:1090883-1091247	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr10:1089350-1092506	A549	lung:	n/a	n/a
6	POLR2A	chr10:1090772-1091199	GM12878	blood:	n/a	n/a
7	POLR2A	chr10:1090667-1091057	GM12892	blood:	n/a	n/a
8	POLR2A	chr10:1089458-1091279	Hela-S3	cervix:	n/a	n/a
9	NFATC1	chr10:1089315-1091460	GM12878	blood:	n/a	n/a
10	POLR2A	chr10:1082282-1092534	K562	blood:	n/a	n/a
11	POLR2A	chr10:1090711-1091221	HepG2	liver:	n/a	n/a
12	POLR2A	chr10:1090177-1091054	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr10:1090867-1091197	GM12878	blood:	n/a	n/a
14	POLR2A	chr10:1089306-1091269	HepG2	liver:	n/a	n/a
15	POLR2A	chr10:1090688-1091165	HepG2	liver:	n/a	n/a
16	POLR2A	chr10:1088828-1092481	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr10:1088966-1092589	IMR90	lung:	n/a	n/a
18	HEY1	chr10:1090672-1091199	HepG2	liver:	n/a	n/a
19	RFX5	chr10:1090778-1091055	K562	blood:	n/a	n/a
20	POLR2A	chr10:1089574-1091714	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr10:1089125-1092500	GM12891	blood:	n/a	n/a
22	TAL1	chr10:1090879-1091332	K562	blood:	n/a	n/a
23	POLR2A	chr10:1089294-1091273	GM12878	blood:	n/a	n/a
24	POLR2A	chr10:1089210-1091271	GM12878	blood:	n/a	n/a
25	POLR2A	chr10:1089408-1091204	HepG2	liver:	n/a	n/a
26	POLR2A	chr10:1090849-1091224	PFSK-1	brain:	n/a	n/a
27	NFATC1	chr10:1090719-1091294	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:1090197..1098635-chr10:1098667..1108160,39	K562	blood:
2	chr10:1086551..1092852-chr10:1093358..1097808,14	MCF-7	breast:

No data

Variant related genes	Relation type
WDR37	TF binding region
RNU7-163P	TF binding region
ENSG00000067064	Chromatin interaction
ENSG00000047056	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10508206	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10903358	0.80[AMR][1000 genomes]
rs11250228	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11814057	0.88[ASN][1000 genomes]
rs12762955	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12767171	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777800	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12783621	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12784928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131826	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2127604	1.00[JPT][hapmap]
rs28512382	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34159706	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34884971	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35657988	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4463782	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs66797613	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67205460	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67696450	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7075188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7094905	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7100196	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs71491334	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
3	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
16	nsv1040178	chr10:1024910-1126104	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv540410	chr10:1024910-1126104	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv894722	chr10:1058837-1274538	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
19	nsv1046220	chr10:1064024-1188998	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
20	nsv894723	chr10:1073684-1259485	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
21	nsv5532	chr10:1079499-1101700	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	nsv894724	chr10:1084942-1116294	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7072554	ADARB2	cis	parietal	SCAN
rs7072554	DIP2C	cis	cerebellum	SCAN
rs7072554	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1035000-1094000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:1060000-1091600	Weak transcription	Hela-S3	cervix
3	chr10:1063200-1092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:1073400-1091800	Weak transcription	Fetal Heart	heart
5	chr10:1082600-1094000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:1083400-1092000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr10:1084000-1091600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:1084000-1093400	Weak transcription	Aorta	Aorta
9	chr10:1084200-1093400	Weak transcription	Thymus	Thymus
10	chr10:1084400-1091000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr10:1085000-1091200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr10:1085200-1091400	Weak transcription	Spleen	Spleen
13	chr10:1087000-1092200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:1087600-1091400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:1088000-1093400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr10:1088200-1091000	Weak transcription	Stomach Mucosa	stomach
17	chr10:1088600-1091200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr10:1088800-1091000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr10:1088800-1092000	Weak transcription	Colon Smooth Muscle	Colon
20	chr10:1089200-1091200	Genic enhancers	Liver	Liver
21	chr10:1089200-1092800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr10:1089400-1091000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:1089400-1091600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:1089400-1091600	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
25	chr10:1089400-1093600	Weak transcription	Fetal Kidney	kidney
26	chr10:1089600-1091000	Enhancers	Right Atrium	heart
27	chr10:1089600-1091200	Enhancers	Left Ventricle	heart
28	chr10:1089600-1091400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:1089600-1091600	Enhancers	Fetal Brain Male	brain
30	chr10:1089600-1091600	Weak transcription	Pancreas	Pancrea
31	chr10:1089600-1092200	Weak transcription	Osteobl	bone
32	chr10:1089600-1092600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr10:1089600-1093600	Weak transcription	Placenta	Placenta
34	chr10:1089800-1091400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr10:1089800-1091800	Weak transcription	A549	lung
36	chr10:1089800-1092000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:1089800-1092200	Weak transcription	Colonic Mucosa	Colon
38	chr10:1089800-1092200	Weak transcription	Ovary	ovary
39	chr10:1089800-1092200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr10:1089800-1093400	Weak transcription	Fetal Intestine Small	intestine
41	chr10:1089800-1093400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr10:1090000-1091000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr10:1090000-1091000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:1090000-1091000	Enhancers	Brain Cingulate Gyrus	brain
45	chr10:1090000-1091000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:1090000-1091200	Enhancers	Brain Anterior Caudate	brain
47	chr10:1090000-1091400	Active TSS	GM12878-XiMat	blood
48	chr10:1090000-1091600	Weak transcription	Fetal Lung	lung
49	chr10:1090000-1091600	Enhancers	Fetal Muscle Leg	muscle
50	chr10:1090000-1091600	Weak transcription	Rectal Mucosa Donor 29	rectum

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