Variant report

Variant	rs89278
Chromosome Location	chrX:154842666-154842667
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	YY1	chrX:154842427-154842806	SK-N-SH_RA	brain:	n/a	chrX:154842575-154842586
2	SP1	chrX:154842370-154842848	A549	lung:	n/a	chrX:154842617-154842629 chrX:154842619-154842628 chrX:154842617-154842629 chrX:154842618-154842628 chrX:154842618-154842627 chrX:154842577-154842586 chrX:154842576-154842590 chrX:154842618-154842627
3	POLR2A	chrX:154842091-154842822	A549	lung:	n/a	n/a
4	POLR2A	chrX:154841973-154842771	GM12891	blood:	n/a	n/a
5	POLR2A	chrX:154841964-154842971	K562	blood:	n/a	n/a
6	CREB1	chrX:154841956-154842791	HepG2	liver:	n/a	n/a
7	POLR2A	chrX:154841782-154842989	PBDE	blood:	n/a	n/a
8	POLR2A	chrX:154841927-154842764	GM12878	blood:	n/a	n/a
9	ELK1	chrX:154842338-154842794	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chrX:154841918-154842872	MCF-7	breast:	n/a	n/a
11	POLR2A	chrX:154842045-154842908	K562	blood:	n/a	n/a
12	TAF1	chrX:154842063-154842827	H1-hESC	embryonic stem cell:	n/a	n/a
13	BRCA1	chrX:154842147-154842758	Hela-S3	cervix:	n/a	n/a
14	MAX	chrX:154842472-154842896	MCF-7	breast:	n/a	n/a
15	TBP	chrX:154842113-154842855	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chrX:154842506-154842876	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chrX:154842040-154842675	H1-neurons	neurons:	n/a	n/a
18	TBP	chrX:154842106-154843145	K562	blood:	n/a	n/a
19	MAZ	chrX:154842384-154842810	GM12878	blood:	n/a	n/a
20	POLR2A	chrX:154842218-154842854	HCT-116	colon:	n/a	n/a
21	ELK1	chrX:154842488-154842756	GM12878	blood:	n/a	n/a
22	POLR2A	chrX:154841905-154842888	HepG2	liver:	n/a	n/a
23	POLR2A	chrX:154842412-154842807	SK-N-MC	brain:	n/a	n/a
24	STAT1	chrX:154842240-154842700	GM12878	blood:	n/a	chrX:154842573-154842585
25	POLR2A	chrX:154841952-154842913	HEK293	kidney:	n/a	n/a
26	HMGN3	chrX:154842061-154842799	K562	blood:	n/a	n/a
27	POLR2A	chrX:154842430-154842823	SK-N-SH	brain:	n/a	n/a
28	MXI1	chrX:154841660-154843001	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chrX:154841976-154842893	GM12878	blood:	n/a	n/a
30	IRF1	chrX:154842495-154842819	K562	blood:	n/a	chrX:154842615-154842629
31	YY1	chrX:154842465-154842945	SK-N-SH_RA	brain:	n/a	chrX:154842575-154842586
32	MAX	chrX:154841979-154842826	K562	blood:	n/a	n/a
33	TAF1	chrX:154841978-154842855	ECC-1	luminal epithelium:	n/a	n/a
34	TAF1	chrX:154842140-154842902	A549	lung:	n/a	n/a
35	POLR2A	chrX:154841896-154842817	H1-hESC	embryonic stem cell:	n/a	n/a
36	GABPA	chrX:154842355-154842847	MCF-7	breast:	n/a	n/a
37	BHLHE40	chrX:154842005-154842825	K562	blood:	n/a	n/a
38	UBTF	chrX:154842021-154842963	K562	blood:	n/a	n/a
39	TAF1	chrX:154842037-154842729	HepG2	liver:	n/a	n/a
40	GTF2F1	chrX:154842500-154842705	H1-hESC	embryonic stem cell:	n/a	n/a
41	E2F6	chrX:154842083-154842852	K562	blood:	n/a	n/a
42	POLR2A	chrX:154841988-154842881	GM12892	blood:	n/a	n/a
43	GABPA	chrX:154842512-154842699	HepG2	liver:	n/a	n/a
44	CTCF	chrX:154842647-154842751	K562	blood:	n/a	n/a
45	BHLHE40	chrX:154842475-154842802	GM12878	blood:	n/a	n/a
46	HNF4G	chrX:154842459-154842670	HepG2	liver:	n/a	n/a
47	ZNF143	chrX:154842156-154842733	Hela-S3	cervix:	n/a	n/a
48	E2F6	chrX:154842475-154842797	K562	blood:	n/a	n/a
49	POLR2A	chrX:154841997-154842736	HepG2	liver:	n/a	n/a
50	SP1	chrX:154842326-154842822	A549	lung:	n/a	chrX:154842617-154842629 chrX:154842619-154842628 chrX:154842617-154842629 chrX:154842618-154842628 chrX:154842618-154842627 chrX:154842577-154842586 chrX:154842576-154842590 chrX:154842618-154842627

Variant related genes	Relation type
TMLHE	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10782079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1084450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs473491	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs473529	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs473772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs476928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs479901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs498000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs561928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs574386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs580468	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs5940376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs5940478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5940479	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5940484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5940486	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs5940510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5940539	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs5983658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs5983743	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs628761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs674707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv29972	chrX:154418093-154929412	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv532965	chrX:154418093-155226096	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv532967	chrX:154418093-155252027	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv915940	chrX:154577793-155232907	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv534441	chrX:154664337-155251871	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv519485	chrX:154737376-154929412	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv869305	chrX:154739403-155190347	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription 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	7 gene(s)	inside rSNPs	diseases
8	nsv916736	chrX:154762193-155232894	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv520699	chrX:154774663-154929412	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154840800-154843000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chrX:154840800-154843000	Active TSS	Brain Substantia Nigra	brain
3	chrX:154840800-154843000	Active TSS	GM12878-XiMat	blood
4	chrX:154840800-154843000	Active TSS	NHLF	lung
5	chrX:154840800-154843200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chrX:154841000-154842800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chrX:154841000-154842800	Active TSS	Rectal Mucosa Donor 31	rectum
8	chrX:154841000-154842800	Active TSS	Osteobl	bone
9	chrX:154841000-154843000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chrX:154841000-154843000	Active TSS	Primary hematopoietic stem cells	blood
11	chrX:154841000-154843000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chrX:154841000-154843000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chrX:154841000-154843000	Active TSS	Brain Germinal Matrix	brain
14	chrX:154841000-154843000	Active TSS	Rectal Smooth Muscle	rectum
15	chrX:154841000-154843000	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chrX:154841000-154843000	Active TSS	HSMM	muscle
17	chrX:154841000-154843000	Active TSS	HSMMtube	muscle
18	chrX:154841000-154843200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chrX:154841000-154843200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chrX:154841000-154843200	Active TSS	Brain Hippocampus Middle	brain
21	chrX:154841000-154843200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chrX:154841200-154842800	Active TSS	Muscle Satellite Cultured Cells	--
23	chrX:154841200-154842800	Active TSS	Fetal Intestine Small	intestine
24	chrX:154841200-154842800	Active TSS	Hela-S3	cervix
25	chrX:154841200-154842800	Active TSS	NH-A	brain
26	chrX:154841200-154843000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chrX:154841200-154843000	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chrX:154841200-154843000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chrX:154841200-154843000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chrX:154841200-154843000	Active TSS	Colonic Mucosa	Colon
31	chrX:154841200-154843000	Active TSS	Colon Smooth Muscle	Colon
32	chrX:154841200-154843000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chrX:154841200-154843000	Active TSS	Left Ventricle	heart
34	chrX:154841200-154843000	Active TSS	Thymus	Thymus
35	chrX:154841200-154843000	Active TSS	HUVEC	blood vessel
36	chrX:154841200-154843000	Active TSS	NHDF-Ad	bronchial
37	chrX:154841200-154843200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chrX:154841200-154843200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chrX:154841200-154843200	Active TSS	Primary monocytes fromperipheralblood	blood
40	chrX:154841200-154843200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chrX:154841200-154843200	Active TSS	Duodenum Mucosa	Duodenum
42	chrX:154841200-154843200	Active TSS	Fetal Brain Female	brain
43	chrX:154841200-154843200	Active TSS	Fetal Kidney	kidney
44	chrX:154841200-154843200	Active TSS	A549	lung
45	chrX:154841200-154843200	Active TSS	HMEC	breast
46	chrX:154841200-154843200	Active TSS	K562	blood
47	chrX:154841200-154843200	Active TSS	Monocytes-CD14+_RO01746	blood
48	chrX:154841400-154842800	Active TSS	Primary T cells fromperipheralblood	blood
49	chrX:154841400-154842800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chrX:154841400-154842800	Active TSS	Placenta	Placenta

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