Variant report

Variant	rs5981325
Chromosome Location	chrX:74376420-74376421
allele	C/T
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	ELK1	chrX:74376024-74376528	GM12878	blood:	n/a	chrX:74376214-74376223 chrX:74376214-74376223
2	POLR2A	chrX:74375348-74376661	Hela-S3	cervix:	n/a	n/a
3	TAF1	chrX:74375701-74376446	GM12878	blood:	n/a	n/a
4	POLR2A	chrX:74375699-74376566	Hela-S3	cervix:	n/a	n/a
5	SIN3A	chrX:74375587-74376506	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chrX:74375716-74376621	SK-N-SH_RA	brain:	n/a	chrX:74376525-74376535
7	MTA3	chrX:74375736-74376503	GM12878	blood:	n/a	n/a
8	GABPA	chrX:74375821-74376623	MCF-7	breast:	n/a	n/a
9	MAZ	chrX:74375886-74376453	HepG2	liver:	n/a	n/a
10	ELF1	chrX:74375823-74376461	MCF-7	breast:	n/a	chrX:74376210-74376223
11	GATA2	chrX:74375896-74376800	SH-SY5Y	brain:	n/a	chrX:74376547-74376557 chrX:74376135-74376148 chrX:74376541-74376562 chrX:74376548-74376555 chrX:74376548-74376555 chrX:74376544-74376560 chrX:74376548-74376555
12	GABPA	chrX:74375890-74376461	SK-N-SH	brain:	n/a	n/a
13	KAP1	chrX:74375860-74376855	U2OS	brain:	n/a	chrX:74376121-74376129
14	POLR2A	chrX:74375654-74376506	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chrX:74375662-74376478	PFSK-1	brain:	n/a	n/a
16	POLR2A	chrX:74375322-74376898	GM12878	blood:	n/a	n/a
17	SPI1	chrX:74375646-74376494	GM12878	blood:	n/a	n/a
18	TCF7L2	chrX:74375969-74376835	HEK293	kidney:	n/a	n/a
19	YY1	chrX:74375652-74376438	A549	lung:	n/a	n/a
20	YY1	chrX:74375631-74376596	SK-N-SH	brain:	n/a	chrX:74376525-74376535
21	GABPA	chrX:74375938-74376457	MCF-7	breast:	n/a	n/a
22	CEBPB	chrX:74376300-74376868	IMR90	lung:	n/a	n/a
23	POLR2A	chrX:74375871-74376444	GM12878	blood:	n/a	n/a
24	POLR2A	chrX:74375009-74376653	PBDE	blood:	n/a	n/a
25	TBP	chrX:74375872-74376677	GM12878	blood:	n/a	n/a
26	POLR2A	chrX:74375337-74376448	GM19099	blood:	n/a	n/a
27	CTCF	chrX:74376360-74376510	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chrX:74375537-74376460	GM18505	blood:	n/a	n/a
29	GABPA	chrX:74375907-74376501	A549	lung:	n/a	n/a
30	ELK4	chrX:74375991-74376685	Hela-S3	cervix:	n/a	chrX:74376214-74376222 chrX:74376213-74376224 chrX:74376214-74376223
31	GATA3	chrX:74376313-74376687	SH-SY5Y	brain:	n/a	chrX:74376547-74376557 chrX:74376541-74376562 chrX:74376548-74376555 chrX:74376548-74376555 chrX:74376544-74376560 chrX:74376548-74376555
32	ELF1	chrX:74375968-74376434	HepG2	liver:	n/a	chrX:74376210-74376223
33	TCF7L2	chrX:74375731-74376775	Hela-S3	cervix:	n/a	n/a
34	GTF2F1	chrX:74375393-74376503	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chrX:74375684-74376487	HepG2	liver:	n/a	n/a
36	POLR2A	chrX:74375700-74376440	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chrX:74375870-74376456	SK-N-SH	brain:	n/a	n/a
38	HCFC1	chrX:74375746-74377101	Hela-S3	cervix:	n/a	n/a
39	ELK1	chrX:74376014-74376616	Hela-S3	cervix:	n/a	chrX:74376214-74376223 chrX:74376214-74376223
40	MAX	chrX:74375386-74376691	Hela-S3	cervix:	n/a	n/a
41	TAF1	chrX:74375668-74376473	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chrX:74375904-74376448	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chrX:74375328-74376769	GM12891	blood:	n/a	n/a
44	CEBPB	chrX:74375881-74376876	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chrX:74375415-74376593	Raji	blood:	n/a	n/a
46	POLR2A	chrX:74375393-74376446	MCF10A-Er-Src	breast:	n/a	n/a
47	ELF1	chrX:74375944-74376524	HCT-116	colon:	n/a	chrX:74376210-74376223
48	YY1	chrX:74375664-74376433	SK-N-SH	brain:	n/a	n/a
49	TCF7L2	chrX:74375940-74376610	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chrX:74375793-74376422	GM19193	blood:	n/a	n/a

Variant related genes	Relation type
ABCB7	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1039123	1.00[YRI][hapmap]
rs1340989	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1340990	0.98[MKK][hapmap]
rs1361702	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1418343	0.82[MKK][hapmap]
rs1472396	0.98[MKK][hapmap]
rs1566126	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4892392	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4892559	1.00[YRI][hapmap]
rs5937962	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs5981761	0.98[MKK][hapmap]
rs5981784	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916758	chrX:73546406-74420929	Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv531128	chrX:74232814-74416887	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv3365132	chrX:74308852-74407212	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv534085	chrX:74360310-74516106	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:74373800-74377200	Active TSS	GM12878-XiMat	blood
2	chrX:74374000-74376800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chrX:74374200-74377000	Active TSS	K562	blood
4	chrX:74374400-74376600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chrX:74374600-74376600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chrX:74374800-74376600	Active TSS	H1 Cell Line	embryonic stem cell
7	chrX:74374800-74376600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chrX:74374800-74376800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chrX:74374800-74376800	Active TSS	Fetal Intestine Large	intestine
10	chrX:74374800-74376800	Active TSS	Stomach Mucosa	stomach
11	chrX:74374800-74376800	Active TSS	NH-A	brain
12	chrX:74374800-74377000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chrX:74374800-74377000	Active TSS	Fetal Brain Female	brain
14	chrX:74374800-74377000	Active TSS	Fetal Muscle Leg	muscle
15	chrX:74374800-74377000	Active TSS	Right Atrium	heart
16	chrX:74374800-74377000	Active TSS	NHDF-Ad	bronchial
17	chrX:74374800-74377200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chrX:74374800-74377200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chrX:74375000-74376600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chrX:74375000-74376600	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chrX:74375000-74376600	Active TSS	HMEC	breast
22	chrX:74375000-74376800	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chrX:74375000-74376800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chrX:74375000-74376800	Active TSS	Brain Substantia Nigra	brain
25	chrX:74375000-74377000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chrX:74375000-74377000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chrX:74375000-74377000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chrX:74375000-74377000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chrX:74375000-74377000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chrX:74375000-74377000	Active TSS	Duodenum Mucosa	Duodenum
31	chrX:74375000-74377000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chrX:74375000-74377200	Active TSS	Rectal Mucosa Donor 29	rectum
33	chrX:74375200-74376600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chrX:74375200-74376600	Active TSS	H9 Cell Line	embryonic stem cell
35	chrX:74375200-74376600	Active TSS	HUVEC	blood vessel
36	chrX:74375200-74376800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chrX:74375200-74376800	Active TSS	Primary B cells from cord blood	blood
38	chrX:74375200-74376800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chrX:74375200-74376800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chrX:74375200-74376800	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chrX:74375200-74376800	Active TSS	Brain Germinal Matrix	brain
42	chrX:74375200-74376800	Active TSS	Brain Hippocampus Middle	brain
43	chrX:74375200-74376800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chrX:74375200-74376800	Active TSS	Fetal Intestine Small	intestine
45	chrX:74375200-74376800	Active TSS	Fetal Kidney	kidney
46	chrX:74375200-74376800	Active TSS	Left Ventricle	heart
47	chrX:74375200-74376800	Active TSS	Right Ventricle	heart
48	chrX:74375200-74376800	Active TSS	Stomach Smooth Muscle	stomach
49	chrX:74375200-74376800	Active TSS	Thymus	Thymus
50	chrX:74375200-74376800	Active TSS	HSMM	muscle

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