Variant report

Variant	rs1930243
Chromosome Location	chr9:103116172-103116173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr9:103112680-103116753	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr9:103114192-103116453	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:103114175-103116583	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:103113860-103116202	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr9:103114501-103116255	Raji	blood:	n/a	n/a
6	POLR2A	chr9:103115891-103116703	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT1	chr9:103116084-103116237	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:103114354-103116279	K562	blood:	n/a	n/a
9	POLR2A	chr9:103114521-103116598	HepG2	liver:	n/a	n/a
10	HCFC1	chr9:103113996-103116234	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:103108889..103112022-chr9:103112659..103116565,8	MCF-7	breast:
2	chr9:103112743..103119519-chr9:103186928..103191502,9	MCF-7	breast:
3	chr9:103112020..103116853-chr9:103187928..103193300,12	MCF-7	breast:
4	chr9:103113279..103116752-chr9:103187119..103190910,6	K562	blood:
5	chr9:103113751..103117482-chr9:103187755..103190910,6	K562	blood:

No data

Variant related genes	Relation type
TEX10	TF binding region
ENSG00000136891	Chromatin interaction
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10117799	0.88[ASN][1000 genomes]
rs10118398	0.98[ASN][1000 genomes]
rs10118701	0.85[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10120244	0.97[ASN][1000 genomes]
rs10123866	0.88[ASN][1000 genomes]
rs10123913	0.88[ASN][1000 genomes]
rs10124133	0.98[ASN][1000 genomes]
rs10124893	0.87[ASN][1000 genomes]
rs10125785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1014651	0.82[JPT][hapmap]
rs1014652	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs10739796	0.82[JPT][hapmap]
rs10760724	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819737	0.82[JPT][hapmap]
rs10819751	0.86[ASN][1000 genomes]
rs10819756	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10819759	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10819761	0.95[ASN][1000 genomes]
rs10819762	0.98[ASN][1000 genomes]
rs10819764	0.98[ASN][1000 genomes]
rs10819767	0.98[ASN][1000 genomes]
rs10989049	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10989056	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10989064	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989067	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989070	0.98[ASN][1000 genomes]
rs11789196	0.88[ASN][1000 genomes]
rs12336751	0.82[JPT][hapmap]
rs12684939	0.92[ASN][1000 genomes]
rs1338121	1.00[CHD][hapmap]
rs1338123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1338124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1338125	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs1415926	0.82[JPT][hapmap]
rs1572607	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1930244	0.91[ASN][1000 genomes]
rs1961367	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999877	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs2026999	0.98[ASN][1000 genomes]
rs2065997	1.00[CHD][hapmap]
rs2151131	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs2210498	0.98[ASN][1000 genomes]
rs2245216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs2417084	0.98[ASN][1000 genomes]
rs2417176	0.98[ASN][1000 genomes]
rs2476441	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2476442	0.82[JPT][hapmap]
rs2485745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2787363	0.82[JPT][hapmap]
rs2787364	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs2787365	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2787368	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[ASN][1000 genomes]
rs2787369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2787371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2787372	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs2787373	0.88[ASN][1000 genomes]
rs2787374	1.00[CHD][hapmap]
rs2787375	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2787376	0.81[ASN][1000 genomes]
rs2787377	0.90[ASN][1000 genomes]
rs2787380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2787381	0.85[ASN][1000 genomes]
rs2787383	0.86[ASN][1000 genomes]
rs2787385	0.85[ASN][1000 genomes]
rs2787388	0.86[ASN][1000 genomes]
rs2787390	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2787391	0.82[JPT][hapmap]
rs2787394	0.82[JPT][hapmap]
rs2787395	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2787396	0.82[JPT][hapmap]
rs2787397	0.91[CHD][hapmap];0.82[JPT][hapmap]
rs2806681	0.83[CHD][hapmap]
rs2806682	0.82[JPT][hapmap]
rs2806684	0.82[JPT][hapmap]
rs2806687	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2806691	1.00[CHD][hapmap]
rs2806692	0.86[ASN][1000 genomes]
rs2806693	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2806694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2806695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs2806696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2806699	1.00[CHD][hapmap]
rs2806700	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs2806702	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2806703	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28464821	0.95[ASN][1000 genomes]
rs3813712	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs3923501	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4128230	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4237194	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4237195	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4237196	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4446782	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742782	0.88[ASN][1000 genomes]
rs4742783	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742784	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4743392	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743393	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4743394	0.95[ASN][1000 genomes]
rs4743395	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4743396	0.98[ASN][1000 genomes]
rs5029342	0.88[ASN][1000 genomes]
rs5029343	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59242794	0.95[ASN][1000 genomes]
rs6479008	0.85[ASN][1000 genomes]
rs6479009	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6479010	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6479011	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6479013	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs6479014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020988	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7021310	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025891	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7025938	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7035619	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7036570	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047694	0.92[ASN][1000 genomes]
rs7048601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7472	0.88[ASN][1000 genomes]
rs7849966	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7852189	0.98[ASN][1000 genomes]
rs7854693	0.88[ASN][1000 genomes]
rs7860513	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864494	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7866850	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869985	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871702	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875775	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846752	0.82[JPT][hapmap]
rs846753	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs846770	0.82[JPT][hapmap]
rs860171	0.82[JPT][hapmap]
rs875522	0.92[YRI][hapmap]
rs914711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299338	0.98[ASN][1000 genomes]
rs944710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs959893	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9775014	0.84[ASN][1000 genomes]
rs9775182	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9886877	0.84[CHD][hapmap];0.82[JPT][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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1930243	INVS	cis	multi-tissue	Pritchard
rs1930243	INVS	cis	Thyroid	GTEx
rs1930243	TEX10	cis	cerebellum	SCAN
rs1930243	TEX10	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103113400-103116400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:103113400-103116800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:103113600-103116200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:103113600-103116400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:103113800-103116200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:103114000-103116200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:103114200-103116200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:103114200-103116200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr9:103114400-103116600	Active TSS	Fetal Lung	lung
10	chr9:103115400-103116200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr9:103115400-103116200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr9:103115400-103116200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr9:103115400-103116400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:103115400-103116400	Flanking Active TSS	Dnd41	blood
15	chr9:103115400-103116600	Flanking Active TSS	HepG2	liver
16	chr9:103115600-103116200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr9:103115600-103116200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr9:103115600-103116200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr9:103115600-103116200	Enhancers	Primary B cells from peripheral blood	blood
20	chr9:103115600-103116200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr9:103115600-103116200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:103115600-103116200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr9:103115600-103116200	Flanking Active TSS	K562	blood
24	chr9:103115600-103116400	Flanking Active TSS	A549	lung
25	chr9:103115800-103116200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:103115800-103116200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:103115800-103116200	Enhancers	Primary hematopoietic stem cells	blood
28	chr9:103115800-103116200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:103115800-103116200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:103115800-103116200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:103115800-103116200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:103115800-103116200	Enhancers	Brain Angular Gyrus	brain
33	chr9:103115800-103116200	Enhancers	Brain Anterior Caudate	brain
34	chr9:103115800-103116200	Enhancers	Brain Substantia Nigra	brain
35	chr9:103115800-103116200	Enhancers	Duodenum Mucosa	Duodenum
36	chr9:103115800-103116200	Flanking Active TSS	Fetal Brain Female	brain
37	chr9:103115800-103116200	Flanking Active TSS	Fetal Heart	heart
38	chr9:103115800-103116200	Enhancers	Fetal Intestine Large	intestine
39	chr9:103115800-103116200	Active TSS	Fetal Intestine Small	intestine
40	chr9:103115800-103116200	Flanking Active TSS	Fetal Kidney	kidney
41	chr9:103115800-103116200	Enhancers	Fetal Muscle Leg	muscle
42	chr9:103115800-103116200	Enhancers	Placenta	Placenta
43	chr9:103115800-103116200	Enhancers	Fetal Thymus	thymus
44	chr9:103115800-103116200	Enhancers	Psoas Muscle	Psoas
45	chr9:103115800-103116200	Flanking Active TSS	Hela-S3	cervix
46	chr9:103115800-103116400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:103115800-103116400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr9:103115800-103116400	Weak transcription	Aorta	Aorta
49	chr9:103115800-103116400	Enhancers	Brain Hippocampus Middle	brain
50	chr9:103115800-103116400	Enhancers	Thymus	Thymus

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