Variant report

Variant	rs10798003
Chromosome Location	chr1:185247794-185247795
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	IRF1	chr1:185247761-185247869	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:185245943..185248403-chr1:185249345..185254666,5	K562	blood:
2	chr1:185247655..185249315-chr1:185250034..185251738,2	MCF-7	breast:
3	chr1:185237694..185239337-chr1:185247474..185249416,2	K562	blood:

Variant related genes	Relation type
ENSG00000238061	TF binding region
ENSG00000238061	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10174	0.92[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs10218496	0.84[ASN][1000 genomes]
rs10752947	0.82[TSI][hapmap]
rs10798002	0.98[EUR][1000 genomes]
rs10798004	0.84[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798006	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911700	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911702	0.92[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs10911704	0.89[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs10911706	0.83[ASN][1000 genomes]
rs10911708	0.85[EUR][1000 genomes]
rs12026391	0.92[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs12041704	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs12096987	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12119471	0.86[ASN][1000 genomes]
rs12127840	0.86[ASN][1000 genomes]
rs12135172	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12135769	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12136040	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336753	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17641003	0.86[EUR][1000 genomes]
rs1889976	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095610	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2152707	0.90[EUR][1000 genomes]
rs2224027	0.81[CEU][hapmap]
rs2295212	0.83[ASN][1000 genomes]
rs2378909	0.92[EUR][1000 genomes]
rs2378910	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs2383269	0.85[ASN][1000 genomes]
rs34611062	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57977436	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424975	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6666742	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6682891	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685627	0.97[EUR][1000 genomes]
rs7123	0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs726567	0.89[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs7512245	0.81[ASN][1000 genomes]
rs7537341	0.91[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7539575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539658	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7542721	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545878	0.81[CEU][hapmap]
rs7550599	0.84[ASN][1000 genomes]
rs7553819	0.82[ASN][1000 genomes]
rs883753	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs9988622	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10798003	IVNS1ABP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185193800-185263600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:185210600-185250400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:185218800-185269400	Weak transcription	Pancreas	Pancrea
4	chr1:185227800-185262000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:185228800-185250400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:185231000-185263400	Weak transcription	Fetal Kidney	kidney
7	chr1:185231800-185249200	Weak transcription	Primary T cells from cord blood	blood
8	chr1:185234000-185253200	Weak transcription	Fetal Heart	heart
9	chr1:185235000-185261800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:185235200-185256800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:185235400-185265400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:185236600-185265600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:185237000-185248000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:185238800-185253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:185239600-185249600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:185239600-185262000	Weak transcription	HSMMtube	muscle
17	chr1:185239800-185250400	Weak transcription	Liver	Liver
18	chr1:185239800-185262000	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:185239800-185263800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:185240000-185265800	Weak transcription	Fetal Lung	lung
21	chr1:185240200-185267200	Weak transcription	Gastric	stomach
22	chr1:185240400-185268800	Weak transcription	Aorta	Aorta
23	chr1:185240800-185250400	Weak transcription	Adipose Nuclei	Adipose
24	chr1:185240800-185273000	Weak transcription	Spleen	Spleen
25	chr1:185241400-185250600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:185241600-185261800	Weak transcription	Fetal Brain Female	brain
27	chr1:185242000-185262000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:185244000-185261400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:185244800-185264800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:185245400-185268800	Weak transcription	Esophagus	oesophagus
31	chr1:185245600-185249800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:185245600-185261000	Weak transcription	Fetal Intestine Large	intestine
33	chr1:185245800-185249600	Weak transcription	Brain Germinal Matrix	brain
34	chr1:185245800-185249800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:185245800-185261600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:185245800-185268400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:185245800-185273000	Weak transcription	Right Ventricle	heart
38	chr1:185246000-185253400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:185246000-185254000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:185246200-185261600	Weak transcription	Lung	lung
41	chr1:185246400-185249400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:185246800-185249600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:185246800-185249800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:185246800-185265600	Weak transcription	NHLF	lung
45	chr1:185247000-185247800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:185247000-185248800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:185247000-185248800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:185247000-185249600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:185247200-185247800	Strong transcription	Ovary	ovary
50	chr1:185247200-185248000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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