Variant report

Variant	rs2728530
Chromosome Location	chrX:153991458-153991459
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	MAX	chrX:153990522-153992266	MCF-7	breast:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
2	CTCF	chrX:153991135-153991494	IMR90	lung:	n/a	n/a
3	CTCF	chrX:153991320-153991470	SK-N-SH_RA	brain:	n/a	n/a
4	POLR2A	chrX:153990709-153991588	A549	lung:	n/a	n/a
5	MAX	chrX:153990801-153992212	MCF-7	breast:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
6	ELK1	chrX:153990807-153991993	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chrX:153990399-153992035	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chrX:153990931-153991473	H1-hESC	embryonic stem cell:	n/a	chrX:153990931-153990945 chrX:153991236-153991248
9	MAX	chrX:153990601-153992202	Hela-S3	cervix:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
10	E2F4	chrX:153990690-153992014	K562	blood:	n/a	chrX:153991088-153991097 chrX:153991095-153991107 chrX:153990994-153991003 chrX:153991094-153991105 chrX:153990865-153990874
11	MXI1	chrX:153990585-153992019	H1-hESC	embryonic stem cell:	n/a	chrX:153991800-153991809 chrX:153991798-153991807
12	MAX	chrX:153990743-153992262	ECC-1	luminal epithelium:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
13	POLR2A	chrX:153990626-153991943	HEK293	kidney:	n/a	n/a
14	REST	chrX:153991086-153991490	K562	blood:	n/a	n/a
15	POLR2A	chrX:153990635-153991900	GM19193	blood:	n/a	n/a
16	YY1	chrX:153990996-153991736	A549	lung:	n/a	chrX:153991236-153991248
17	POLR2A	chrX:153990616-153991935	GM18505	blood:	n/a	n/a
18	POLR2A	chrX:153990233-153992131	K562	blood:	n/a	n/a
19	HMGN3	chrX:153990763-153991614	K562	blood:	n/a	n/a
20	YY1	chrX:153990960-153991505	GM12892	blood:	n/a	chrX:153991236-153991248
21	CTCF	chrX:153991320-153991470	Hela-S3	cervix:	n/a	n/a
22	TAF1	chrX:153990553-153991529	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF1	chrX:153990695-153991653	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chrX:153990514-153991496	U87	brain:	n/a	n/a
25	MYC	chrX:153991028-153991994	GM12878	blood:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
26	MAX	chrX:153990546-153992133	SK-N-SH	brain:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
27	MYC	chrX:153990660-153992186	K562	blood:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
28	MYC	chrX:153990625-153992219	MCF10A-Er-Src	breast:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
29	MYC	chrX:153990622-153992049	H1-hESC	embryonic stem cell:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
30	MAX	chrX:153989850-153992279	K562	blood:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
31	CTCF	chrX:153991320-153991470	GM12869	blood:	n/a	n/a
32	RAD21	chrX:153991310-153991471	K562	blood:	n/a	n/a
33	POLR2A	chrX:153990641-153991866	GM15510	blood:	n/a	n/a
34	ELF1	chrX:153990639-153991904	GM12878	blood:	n/a	chrX:153991807-153991820 chrX:153990882-153990893
35	POLR2A	chrX:153990696-153991591	A549	lung:	n/a	n/a
36	MYC	chrX:153990411-153992189	K562	blood:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
37	POLR2A	chrX:153990595-153991962	NB4	blood:	n/a	n/a
38	CTCF	chrX:153991320-153991470	GM12868	blood:	n/a	n/a
39	NRF1	chrX:153990635-153991472	SK-N-SH	brain:	n/a	chrX:153990993-153991004 chrX:153990864-153990875 chrX:153990995-153991004 chrX:153990864-153990878 chrX:153990863-153990874 chrX:153990993-153991007 chrX:153990993-153991002
40	CTCF	chrX:153991320-153991470	WERI-Rb-1	eye:	n/a	n/a
41	CTCF	chrX:153991197-153991522	GM12878	blood:	n/a	n/a
42	POLR2A	chrX:153990512-153991506	K562	blood:	n/a	n/a
43	E2F6	chrX:153990814-153991499	K562	blood:	n/a	chrX:153991088-153991097 chrX:153991095-153991107 chrX:153990994-153991003 chrX:153990865-153990874
44	POLR2A	chrX:153990538-153992103	GM12892	blood:	n/a	n/a
45	MYC	chrX:153990875-153992148	HUVEC	blood vessel:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
46	POLR2A	chrX:153990612-153991557	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chrX:153990533-153992026	K562	blood:	n/a	chrX:153991797-153991810 chrX:153991798-153991809 chrX:153991799-153991808 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809 chrX:153991798-153991808 chrX:153991799-153991808 chrX:153991798-153991809
48	POLR2A	chrX:153990637-153991937	GM18951	blood:	n/a	n/a
49	POLR2A	chrX:153990547-153992341	GM12878	blood:	n/a	n/a
50	POLR2A	chrX:153990544-153992159	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chrX:153625731..153628141-chrX:153991009..153993068,2	K562	blood:
2	chrX:153990073..153992547-chrX:154032098..154033920,3	MCF-7	breast:
3	chrX:153990595..153992573-chrX:154019539..154022418,3	MCF-7	breast:
4	chrX:153990321..153992649-chrX:154019523..154021141,3	MCF-7	breast:
5	chrX:153977025..153984575-chrX:153984728..153992714,22	K562	blood:
6	chrX:153989743..153993040-chrX:153994731..153999132,7	MCF-7	breast:
7	chrX:153770257..153772733-chrX:153989355..153991758,2	K562	blood:
8	chr17:56735244..56737894-chrX:153991021..153993360,2	K562	blood:
9	chr5:81267614..81268129-chrX:153990983..153991950,2	Hela-S3	cervix:
10	X:153989469-153994716..X:154053104-154056925	GM12878	blood:
11	X:153989469-153994716..X:154140465-154148278	K562	blood:
12	chrX:153597771..153599703-chrX:153989259..153992360,3	K562	blood:
13	X:153719993-153730954..X:153989469-153994716	K562	blood:
14	chrX:153989640..153999941-chrX:154001277..154007820,19	MCF-7	breast:
15	chrX:153989931..153993439-chrX:154009341..154014143,4	MCF-7	breast:
16	X:153614328-153625659..X:153989469-153994716	K562	blood:
17	chrX:153774347..153776680-chrX:153991117..153995343,5	MCF-7	breast:

Variant related genes	Relation type
DKC1	TF binding region
ENSG00000147403	Chromatin interaction
ENSG00000237859	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000130830	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000203870	Chromatin interaction
ENSG00000152348	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000130826	Chromatin interaction
ENSG00000206693	Chromatin interaction
ENSG00000160219	Chromatin interaction
ENSG00000206948	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10127172	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[MKK][hapmap]
rs17281377	1.00[LWK][hapmap]
rs1848763	0.89[CHB][hapmap]
rs2664170	0.89[CHB][hapmap]
rs2728526	0.89[CHB][hapmap]
rs2728725	0.89[CHB][hapmap]
rs2728727	1.00[LWK][hapmap]
rs28835013	0.85[ASW][hapmap];1.00[MEX][hapmap]
rs4326559	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[MKK][hapmap]
rs4431759	0.85[ASW][hapmap];1.00[CHB][hapmap];0.83[MKK][hapmap]
rs4526543	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[MKK][hapmap]
rs5945222	0.85[ASW][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];0.86[MKK][hapmap]
rs5945223	1.00[CHB][hapmap]
rs5945224	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[MKK][hapmap]
rs5987005	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[MKK][hapmap]
rs5987011	0.85[ASW][hapmap];1.00[CHB][hapmap];0.83[MKK][hapmap]
rs5987015	0.89[CHB][hapmap]
rs5987016	0.89[CHB][hapmap]
rs6643615	0.85[ASW][hapmap];1.00[CHB][hapmap]
rs6643620	0.85[ASW][hapmap]
rs6643714	0.85[ASW][hapmap];0.88[MEX][hapmap]
rs884840	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[MKK][hapmap]

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153990000-153991800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chrX:153990000-153992800	Active TSS	Duodenum Mucosa	Duodenum
3	chrX:153990000-153993000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chrX:153990200-153991800	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chrX:153990200-153991800	Active TSS	Monocytes-CD14+_RO01746	blood
6	chrX:153990200-153992400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chrX:153990200-153992400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chrX:153990200-153992400	Active TSS	Colonic Mucosa	Colon
9	chrX:153990200-153992400	Active TSS	Fetal Brain Female	brain
10	chrX:153990200-153992400	Active TSS	Thymus	Thymus
11	chrX:153990200-153992600	Active TSS	Fetal Intestine Small	intestine
12	chrX:153990200-153992800	Active TSS	Muscle Satellite Cultured Cells	--
13	chrX:153990200-153993000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chrX:153990200-153993200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chrX:153990200-153994200	Active TSS	GM12878-XiMat	blood
16	chrX:153990400-153991600	Active TSS	Brain Angular Gyrus	brain
17	chrX:153990400-153991800	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chrX:153990400-153991800	Active TSS	Brain Anterior Caudate	brain
19	chrX:153990400-153991800	Active TSS	Brain Cingulate Gyrus	brain
20	chrX:153990400-153991800	Active TSS	Rectal Mucosa Donor 31	rectum
21	chrX:153990400-153991800	Active TSS	Rectal Smooth Muscle	rectum
22	chrX:153990400-153991800	Active TSS	K562	blood
23	chrX:153990400-153991800	Active TSS	NHLF	lung
24	chrX:153990400-153992000	Active TSS	Brain Hippocampus Middle	brain
25	chrX:153990400-153992000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chrX:153990400-153992200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chrX:153990400-153992200	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chrX:153990400-153992200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chrX:153990400-153992200	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chrX:153990400-153992200	ZNF genes & repeats	Fetal Brain Male	brain
31	chrX:153990400-153992200	Active TSS	Fetal Muscle Trunk	muscle
32	chrX:153990400-153992400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chrX:153990400-153992400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chrX:153990400-153992400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chrX:153990400-153992400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chrX:153990400-153992400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chrX:153990400-153992400	Active TSS	Primary T cells from cord blood	blood
38	chrX:153990400-153992400	Active TSS	Brain Inferior Temporal Lobe	brain
39	chrX:153990400-153992400	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chrX:153990400-153992400	Active TSS	Fetal Stomach	stomach
41	chrX:153990400-153992400	Active TSS	Psoas Muscle	Psoas
42	chrX:153990400-153992400	Active TSS	Right Ventricle	heart
43	chrX:153990400-153992400	Active TSS	NHDF-Ad	bronchial
44	chrX:153990400-153992600	Active TSS	Brain Germinal Matrix	brain
45	chrX:153990400-153992800	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chrX:153990400-153992800	Active TSS	H1 Cell Line	embryonic stem cell
47	chrX:153990400-153992800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chrX:153990400-153992800	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chrX:153990400-153992800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chrX:153990400-153993000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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