Variant report

Variant	rs9422541
Chromosome Location	chr10:44064778-44064779
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	POLR2A	chr10:44064164-44065253	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr10:44064638-44064840	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:44063474..44065679-chr10:44068799..44071087,3	MCF-7	breast:
2	chr10:44064124..44067516-chr10:44100353..44103701,5	MCF-7	breast:

Variant related genes	Relation type
ZNF239	TF binding region
ENSG00000198298	Chromatin interaction
ENSG00000196793	Chromatin interaction
ENSG00000232004	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10793442	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10793443	0.95[ASN][1000 genomes]
rs10899827	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10899828	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11238585	0.92[ASN][1000 genomes]
rs11238588	0.88[CHB][hapmap];0.95[ASN][1000 genomes]
rs12354445	0.94[ASN][1000 genomes]
rs12415781	0.83[ASN][1000 genomes]
rs12784891	0.99[ASN][1000 genomes]
rs1338565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1832470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2230660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2230661	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs2393938	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2393939	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2393942	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2393959	0.94[ASN][1000 genomes]
rs2393960	0.94[ASN][1000 genomes]
rs2860340	0.94[ASN][1000 genomes]
rs2999270	0.92[ASN][1000 genomes]
rs2999271	0.94[ASN][1000 genomes]
rs2999272	0.94[ASN][1000 genomes]
rs2999273	0.90[ASN][1000 genomes]
rs2999274	0.94[ASN][1000 genomes]
rs2999277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2999278	0.94[ASN][1000 genomes]
rs2999279	0.94[ASN][1000 genomes]
rs2999280	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3006379	0.94[ASN][1000 genomes]
rs3006380	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006383	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006384	0.94[ASN][1000 genomes]
rs3006385	0.95[ASN][1000 genomes]
rs3763789	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4948747	0.90[ASN][1000 genomes]
rs6593359	0.91[ASN][1000 genomes]
rs7078691	0.95[ASN][1000 genomes]
rs7079328	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7086537	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs7089577	0.92[ASN][1000 genomes]
rs7091995	0.94[ASN][1000 genomes]
rs7092156	0.92[ASN][1000 genomes]
rs7101356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7893169	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7894102	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7897611	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7906129	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7913084	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7915227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9326506	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9422385	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9422388	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9422540	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9422543	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9422544	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9422545	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9422546	0.94[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9422547	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9422549	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9422550	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9422555	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9422557	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798523	chr10:44051698-44070754	Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9422541	ZNF239	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44050400-44069200	Weak transcription	Fetal Thymus	thymus
2	chr10:44053000-44069000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:44053000-44069200	Weak transcription	Thymus	Thymus
4	chr10:44053200-44066600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr10:44053200-44068400	Weak transcription	NHDF-Ad	bronchial
6	chr10:44053200-44068800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:44053200-44068800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:44053200-44068800	Weak transcription	Hela-S3	cervix
9	chr10:44053200-44068800	Weak transcription	HSMMtube	muscle
10	chr10:44053400-44068800	Weak transcription	Brain Substantia Nigra	brain
11	chr10:44053600-44068200	Weak transcription	Fetal Kidney	kidney
12	chr10:44053600-44068600	Weak transcription	NH-A	brain
13	chr10:44053600-44068800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr10:44053600-44068800	Weak transcription	Psoas Muscle	Psoas
15	chr10:44053600-44068800	Weak transcription	Right Ventricle	heart
16	chr10:44053600-44069000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:44053600-44069200	Weak transcription	Left Ventricle	heart
18	chr10:44053800-44066600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr10:44053800-44068600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr10:44053800-44068800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr10:44053800-44069000	Weak transcription	HSMM	muscle
22	chr10:44054200-44069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr10:44054400-44066400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:44055000-44069000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr10:44055000-44069000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr10:44055000-44069600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:44055200-44068800	Weak transcription	Fetal Brain Male	brain
28	chr10:44055400-44070000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr10:44056000-44068400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr10:44056000-44068800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:44056200-44069000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr10:44056200-44069400	Weak transcription	Gastric	stomach
33	chr10:44056800-44066600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr10:44056800-44067000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr10:44057200-44067000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:44057400-44068600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr10:44057600-44065600	Weak transcription	Esophagus	oesophagus
38	chr10:44057600-44065800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:44057600-44066600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:44058000-44065800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr10:44058200-44069200	Weak transcription	A549	lung
42	chr10:44059200-44068800	Weak transcription	Small Intestine	intestine
43	chr10:44059600-44065000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr10:44059600-44069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:44059800-44066400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr10:44059800-44068800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr10:44059800-44068800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:44059800-44069200	Weak transcription	Pancreas	Pancrea
49	chr10:44060800-44066000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:44061400-44065800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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