Variant report

Variant	rs7904928
Chromosome Location	chr10:50508613-50508614
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	POLR2A	chr10:50506647-50509010	K562	blood:	n/a	n/a
2	TBP	chr10:50508013-50509134	K562	blood:	n/a	n/a
3	HEY1	chr10:50506923-50509008	K562	blood:	n/a	n/a
4	CTCF	chr10:50508611-50508821	K562	blood:	n/a	n/a
5	IRF1	chr10:50507843-50509080	K562	blood:	n/a	chr10:50508076-50508090
6	CEBPD	chr10:50508041-50509076	K562	blood:	n/a	n/a
7	MAX	chr10:50506505-50508917	K562	blood:	n/a	n/a
8	GATA1	chr10:50508329-50508941	K562	blood:	n/a	chr10:50508642-50508652
9	RCOR1	chr10:50508066-50509018	K562	blood:	n/a	n/a
10	ELK1	chr10:50508291-50509023	K562	blood:	n/a	n/a
11	UBTF	chr10:50506546-50509056	K562	blood:	n/a	n/a
12	MEF2A	chr10:50508513-50509003	K562	blood:	n/a	chr10:50508763-50508777 chr10:50508761-50508777 chr10:50508765-50508774 chr10:50508762-50508777 chr10:50508763-50508778 chr10:50508757-50508772 chr10:50508764-50508775 chr10:50508758-50508779 chr10:50508762-50508778 chr10:50508765-50508776 chr10:50508758-50508779
13	RCOR1	chr10:50506480-50509331	K562	blood:	n/a	n/a
14	HCFC1	chr10:50506971-50509100	K562	blood:	n/a	n/a
15	CTCF	chr10:50508490-50508927	K562	blood:	n/a	n/a
16	GABPA	chr10:50508464-50508975	K562	blood:	n/a	n/a
17	TRIM28	chr10:50508013-50509092	K562	blood:	n/a	chr10:50508957-50508965
18	CTCF	chr10:50508408-50509066	K562	blood:	n/a	n/a
19	SMC3	chr10:50508559-50508866	K562	blood:	n/a	n/a
20	HEY1	chr10:50508499-50508948	K562	blood:	n/a	n/a
21	MYC	chr10:50508166-50508956	K562	blood:	n/a	n/a
22	UBTF	chr10:50505840-50509021	K562	blood:	n/a	n/a
23	EP300	chr10:50508064-50508993	K562	blood:	n/a	n/a
24	EP300	chr10:50506285-50508997	K562	blood:	n/a	n/a
25	NR2F2	chr10:50508173-50509000	K562	blood:	n/a	n/a
26	TBL1XR1	chr10:50506821-50509004	K562	blood:	n/a	n/a
27	POLR2A	chr10:50506948-50509008	K562	blood:	n/a	n/a
28	ZBTB7A	chr10:50508522-50509007	K562	blood:	n/a	n/a
29	HDAC2	chr10:50508544-50508953	K562	blood:	n/a	n/a
30	PML	chr10:50507905-50509060	K562	blood:	n/a	chr10:50508957-50508965
31	BACH1	chr10:50508137-50509075	K562	blood:	n/a	n/a
32	CBX3	chr10:50508489-50508962	K562	blood:	n/a	n/a
33	CUX1	chr10:50506966-50509165	K562	blood:	n/a	n/a
34	POU2F2	chr10:50507859-50508618	GM12878	blood:	n/a	chr10:50508351-50508364
35	GTF2F1	chr10:50506825-50508897	K562	blood:	n/a	n/a
36	RAD21	chr10:50508536-50508936	K562	blood:	n/a	n/a
37	CTCF	chr10:50508491-50508886	K562	blood:	n/a	n/a
38	RFX5	chr10:50508127-50508834	K562	blood:	n/a	n/a
39	HDAC2	chr10:50508491-50509270	K562	blood:	n/a	n/a
40	CEBPB	chr10:50508134-50508981	K562	blood:	n/a	n/a
41	MXI1	chr10:50507611-50508910	K562	blood:	n/a	n/a
42	MXI1	chr10:50507805-50508819	GM12878	blood:	n/a	n/a
43	RAD21	chr10:50507440-50509485	SK-N-SH	brain:	n/a	chr10:50509161-50509180
44	NR2F2	chr10:50507794-50509266	K562	blood:	n/a	n/a
45	POLR2A	chr10:50505984-50509599	K562	blood:	n/a	n/a
46	CTCF	chr10:50508580-50508730	K562	blood:	n/a	n/a
47	ZNF384	chr10:50507462-50509064	K562	blood:	n/a	n/a
48	POLR2A	chr10:50506790-50509104	K562	blood:	n/a	n/a
49	MAZ	chr10:50506195-50509256	K562	blood:	n/a	n/a
50	EP300	chr10:50508524-50508917	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:50384432..50385996-chr10:50507928..50509644,2	K562	blood:
2	chr10:50322533..50324257-chr10:50507150..50509486,2	K562	blood:
3	chr10:50384969..50387621-chr10:50504946..50509741,4	K562	blood:
4	chr10:50451424..50453022-chr10:50507349..50510137,2	K562	blood:
5	chr10:49863839..49866724-chr10:50507173..50508742,2	K562	blood:
6	chr10:50477578..50479139-chr10:50508412..50510306,2	K562	blood:

Variant related genes	Relation type
C10orf71-AS1	TF binding region
ENSG00000204161	Chromatin interaction
ENSG00000128805	Chromatin interaction
ENSG00000165633	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1001338	0.87[ASN][1000 genomes]
rs11101077	0.87[ASN][1000 genomes]
rs11816487	0.87[ASN][1000 genomes]
rs11817954	0.87[ASN][1000 genomes]
rs17176642	0.87[ASN][1000 genomes]
rs17176649	0.87[ASN][1000 genomes]
rs17176677	0.87[ASN][1000 genomes]
rs17774672	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17783271	0.87[ASN][1000 genomes]
rs2377968	0.87[ASN][1000 genomes]
rs2377970	0.87[ASN][1000 genomes]
rs2377971	0.87[ASN][1000 genomes]
rs2377972	0.87[ASN][1000 genomes]
rs2889804	0.87[ASN][1000 genomes]
rs4409751	0.87[ASN][1000 genomes]
rs4440951	0.87[ASN][1000 genomes]
rs4838379	0.87[ASN][1000 genomes]
rs4838490	0.87[ASN][1000 genomes]
rs4838491	0.87[ASN][1000 genomes]
rs4838495	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537521	0.87[ASN][1000 genomes]
rs6537522	0.87[ASN][1000 genomes]
rs7900404	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7900538	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906537	0.87[ASN][1000 genomes]
rs7919151	1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv895376	chr10:50480164-50557211	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50504800-50511200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:50505800-50509000	Flanking Active TSS	Fetal Muscle Leg	muscle
3	chr10:50505800-50509600	Flanking Active TSS	K562	blood
4	chr10:50506600-50509200	Enhancers	Primary B cells from peripheral blood	blood
5	chr10:50506600-50509200	Enhancers	Fetal Stomach	stomach
6	chr10:50506800-50509200	Enhancers	Primary hematopoietic stem cells	blood
7	chr10:50507000-50509200	Enhancers	GM12878-XiMat	blood
8	chr10:50507200-50509000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr10:50507200-50509000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:50507200-50511200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:50507200-50511400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:50507400-50509000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:50507400-50513800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
14	chr10:50507600-50508800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:50507600-50508800	Enhancers	Brain Germinal Matrix	brain
16	chr10:50507600-50509000	Enhancers	Brain Cingulate Gyrus	brain
17	chr10:50507600-50509800	Enhancers	Placenta	Placenta
18	chr10:50507600-50511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:50507800-50508800	Weak transcription	Adipose Nuclei	Adipose
20	chr10:50507800-50508800	Enhancers	Duodenum Mucosa	Duodenum
21	chr10:50507800-50509200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:50507800-50511800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr10:50508000-50508800	Enhancers	Fetal Brain Male	brain
24	chr10:50508000-50508800	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr10:50508000-50509200	Enhancers	Pancreas	Pancrea
26	chr10:50508000-50509400	Flanking Active TSS	Fetal Heart	heart
27	chr10:50508200-50511200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr10:50508400-50508800	Enhancers	Lung	lung
29	chr10:50508400-50509200	Flanking Active TSS	Fetal Muscle Trunk	muscle
30	chr10:50508400-50509200	Enhancers	Spleen	Spleen
31	chr10:50508600-50508800	Flanking Active TSS	Psoas Muscle	Psoas
32	chr10:50508600-50508800	Flanking Active TSS	HSMMtube	muscle
33	chr10:50508600-50509000	Enhancers	Right Atrium	heart
34	chr10:50508600-50509200	Flanking Active TSS	Right Ventricle	heart
35	chr10:50508600-50509400	Flanking Active TSS	Left Ventricle	heart

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