Variant report

Variant	rs12359825
Chromosome Location	chr10:43950981-43950982
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	chr10:43950654-43951581	ECC-1	luminal epithelium:	n/a	n/a
2	SP1	chr10:43950641-43951603	HCT-116	colon:	n/a	chr10:43951193-43951205 chr10:43951190-43951204 chr10:43951012-43951021 chr10:43951193-43951205 chr10:43951195-43951204 chr10:43951194-43951203 chr10:43951010-43951022 chr10:43951194-43951204 chr10:43951010-43951022
3	MAX	chr10:43950743-43951538	Hela-S3	cervix:	n/a	chr10:43951194-43951204
4	POLR2A	chr10:43950773-43951120	HepG2	liver:	n/a	n/a
5	WRNIP1	chr10:43950764-43951540	GM12878	blood:	n/a	n/a
6	NFIC	chr10:43950660-43951574	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr10:43950750-43951575	HepG2	liver:	n/a	n/a
8	JUND	chr10:43950847-43951389	HepG2	liver:	n/a	n/a
9	ELF1	chr10:43950702-43951569	HepG2	liver:	n/a	chr10:43951181-43951193 chr10:43951191-43951203
10	MBD4	chr10:43950688-43951097	HepG2	liver:	n/a	n/a
11	MYC	chr10:43950726-43951860	K562	blood:	n/a	chr10:43951194-43951204 chr10:43951662-43951671
12	POLR2A	chr10:43950734-43951527	GM12878	blood:	n/a	n/a
13	USF1	chr10:43950704-43951274	A549	lung:	n/a	n/a
14	CTCF	chr10:43950940-43951090	AG04449	skin:	n/a	n/a
15	RCOR1	chr10:43950777-43951524	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr10:43950176-43951572	GM12891	blood:	n/a	n/a
17	ETS1	chr10:43950769-43951528	K562	blood:	n/a	chr10:43951416-43951432 chr10:43951348-43951359
18	POLR2A	chr10:43950592-43951582	Hela-S3	cervix:	n/a	n/a
19	ZKSCAN1	chr10:43950817-43951675	Hela-S3	cervix:	n/a	n/a
20	NRF1	chr10:43950930-43951362	Hela-S3	cervix:	n/a	chr10:43951107-43951118 chr10:43951108-43951119 chr10:43951108-43951117 chr10:43951108-43951122 chr10:43951110-43951119 chr10:43951105-43951119
21	CREB1	chr10:43950771-43951409	A549	lung:	n/a	n/a
22	JUN	chr10:43950822-43951476	H1-hESC	embryonic stem cell:	n/a	chr10:43950832-43950841
23	HCFC1	chr10:43950722-43951520	K562	blood:	n/a	n/a
24	HDAC2	chr10:43950765-43951469	HepG2	liver:	n/a	chr10:43951108-43951117 chr10:43951110-43951119
25	RFX5	chr10:43950851-43951788	K562	blood:	n/a	n/a
26	EP300	chr10:43950624-43951650	A549	lung:	n/a	chr10:43951187-43951203
27	POLR2A	chr10:43950752-43951490	GM10847	blood:	n/a	n/a
28	MAX	chr10:43950709-43951583	K562	blood:	n/a	chr10:43951194-43951204
29	RUNX3	chr10:43950596-43951511	GM12878	blood:	n/a	chr10:43950944-43950953 chr10:43950944-43950953
30	STAT1	chr10:43950761-43951797	GM12878	blood:	n/a	n/a
31	ELF1	chr10:43950688-43951614	MCF-7	breast:	n/a	chr10:43951181-43951193 chr10:43951191-43951203
32	IRF4	chr10:43950733-43951466	GM12878	blood:	n/a	n/a
33	STAT5A	chr10:43950648-43951537	K562	blood:	n/a	n/a
34	ATF1	chr10:43950793-43951427	K562	blood:	n/a	n/a
35	POLR2A	chr10:43950714-43951570	GM18505	blood:	n/a	n/a
36	POLR2A	chr10:43950654-43951567	HepG2	liver:	n/a	n/a
37	CTCF	chr10:43950900-43951050	AG09309	skin:	n/a	n/a
38	POLR2A	chr10:43950495-43951641	PFSK-1	brain:	n/a	n/a
39	ELF1	chr10:43950595-43951836	GM12878	blood:	n/a	chr10:43951181-43951193 chr10:43951191-43951203
40	POLR2A	chr10:43950657-43951515	A549	lung:	n/a	n/a
41	ZBTB7A	chr10:43950764-43951433	K562	blood:	n/a	chr10:43950983-43950990
42	MYC	chr10:43950848-43951435	HUVEC	blood vessel:	n/a	chr10:43951194-43951204
43	RAD21	chr10:43950725-43951634	ECC-1	luminal epithelium:	n/a	n/a
44	ATF3	chr10:43950811-43951427	A549	lung:	n/a	n/a
45	ELF1	chr10:43950742-43951482	A549	lung:	n/a	chr10:43951181-43951193 chr10:43951191-43951203
46	MAZ	chr10:43950761-43951466	Hela-S3	cervix:	n/a	chr10:43951194-43951204
47	TCF12	chr10:43950679-43951532	ECC-1	luminal epithelium:	n/a	n/a
48	MBD4	chr10:43950641-43951364	HepG2	liver:	n/a	n/a
49	BCL3	chr10:43950596-43951564	A549	lung:	n/a	chr10:43951546-43951559 chr10:43951198-43951211
50	MXI1	chr10:43950703-43951451	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:43890245..43893733-chr10:43950048..43952889,6	MCF-7	breast:
2	chr10:43856796..43859444-chr10:43950333..43952475,2	MCF-7	breast:
3	chr10:43930874..43934590-chr10:43949528..43951985,5	K562	blood:
4	chr10:43950502..43951282-chr19:752665..753169,2	Hela-S3	cervix:
5	chr10:43941606..43943262-chr10:43948647..43951071,2	K562	blood:
6	chr10:43930912..43933891-chr10:43949765..43952473,2	MCF-7	breast:
7	chr10:43901812..43907473-chr10:43949275..43952974,10	MCF-7	breast:
8	chr10:43943911..43945434-chr10:43948722..43951171,2	K562	blood:
9	chr10:43901457..43906189-chr10:43948713..43953343,15	MCF-7	breast:
10	chr10:43873108..43875014-chr10:43949897..43951449,2	MCF-7	breast:
11	chr10:43885591..43886523-chr10:43950923..43951849,2	K562	blood:
12	chr10:43936170..43937727-chr10:43949180..43951482,2	K562	blood:
13	chr10:43930995..43932996-chr10:43948327..43951510,4	MCF-7	breast:
14	chr10:43930579..43934633-chr10:43949587..43954210,8	K562	blood:
15	chr10:43943009..43945472-chr10:43950940..43952726,2	MCF-7	breast:
16	chr10:43843617..43844600-chr10:43950622..43951351,3	K562	blood:
17	chr10:43949801..43952727-chr10:43954596..43956488,2	K562	blood:
18	chr10:43950516..43951434-chr11:62413539..62414387,2	Hela-S3	cervix:
19	chr10:43788788..43789350-chr10:43950801..43951694,2	K562	blood:
20	chr10:43932264..43932783-chr10:43950883..43951704,2	MCF-7	breast:
21	chr10:43879008..43883052-chr10:43949060..43952010,4	K562	blood:
22	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:
23	chr10:43870160..43871851-chr10:43949319..43951127,2	K562	blood:
24	chr10:43885901..43886431-chr10:43950839..43951795,3	MCF-7	breast:
25	chr10:43911252..43915931-chr10:43947419..43953058,11	K562	blood:
26	chr10:43627846..43629812-chr10:43949742..43951842,2	MCF-7	breast:
27	chr10:43848475..43851407-chr10:43948589..43951104,3	MCF-7	breast:
28	chr10:43945671..43947485-chr10:43949391..43951784,2	K562	blood:
29	chr10:43902513..43903341-chr10:43950698..43951343,2	HCT-116	colon:

Variant related genes	Relation type
RNU7-193P	TF binding region
ENSG00000243660	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000221400	Chromatin interaction
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11238518	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs11238519	1.00[ASN][1000 genomes]
rs11238520	1.00[ASN][1000 genomes]
rs11238531	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238533	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238547	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238570	1.00[ASN][1000 genomes]
rs11238575	1.00[CHD][hapmap]
rs11238591	1.00[ASN][1000 genomes]
rs11238605	1.00[ASN][1000 genomes]
rs12263722	1.00[ASN][1000 genomes]
rs12354765	0.83[AMR][1000 genomes]
rs12356024	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356570	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359520	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359980	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154006	1.00[ASN][1000 genomes]
rs17154012	1.00[ASN][1000 genomes]
rs17154020	1.00[ASN][1000 genomes]
rs17366560	1.00[ASN][1000 genomes]
rs17447133	1.00[ASN][1000 genomes]
rs17447468	1.00[ASN][1000 genomes]
rs17447580	1.00[ASN][1000 genomes]
rs2999237	1.00[CHD][hapmap]
rs3006389	1.00[CHD][hapmap]
rs3128254	1.00[CHD][hapmap]
rs41313824	1.00[ASN][1000 genomes]
rs4646975	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948720	1.00[ASN][1000 genomes]
rs56120769	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57740712	1.00[ASN][1000 genomes]
rs59220072	1.00[ASN][1000 genomes]
rs60163354	1.00[ASN][1000 genomes]
rs61858993	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858994	0.80[AMR][1000 genomes]
rs61858995	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61859001	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61859177	1.00[ASN][1000 genomes]
rs61859178	1.00[ASN][1000 genomes]
rs61859179	1.00[ASN][1000 genomes]
rs61859180	1.00[ASN][1000 genomes]
rs61859181	1.00[ASN][1000 genomes]
rs61859182	1.00[ASN][1000 genomes]
rs61859185	1.00[ASN][1000 genomes]
rs61859203	1.00[ASN][1000 genomes]
rs61859204	1.00[ASN][1000 genomes]
rs61859441	1.00[ASN][1000 genomes]
rs61859445	1.00[ASN][1000 genomes]
rs61859998	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61860007	1.00[ASN][1000 genomes]
rs61860889	1.00[ASN][1000 genomes]
rs67284218	1.00[ASN][1000 genomes]
rs7073767	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079012	1.00[ASN][1000 genomes]
rs7084706	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093434	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100846	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7900284	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7903467	1.00[ASN][1000 genomes]
rs7905073	1.00[ASN][1000 genomes]
rs7906169	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7906484	1.00[ASN][1000 genomes]
rs7913352	1.00[ASN][1000 genomes]
rs7916345	1.00[ASN][1000 genomes]
rs7920408	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1043746	chr10:43940898-43977155	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43949600-43951400	Active TSS	Right Ventricle	heart
2	chr10:43949800-43951000	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr10:43949800-43951400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:43949800-43951400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr10:43950000-43951400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:43950000-43951400	Active TSS	Thymus	Thymus
7	chr10:43950000-43951400	Active TSS	GM12878-XiMat	blood
8	chr10:43950000-43951400	Active TSS	K562	blood
9	chr10:43950000-43951400	Active TSS	NHDF-Ad	bronchial
10	chr10:43950000-43951600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr10:43950000-43951800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr10:43950000-43951800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr10:43950000-43952000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr10:43950200-43951000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr10:43950200-43951000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr10:43950200-43951200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:43950200-43951200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:43950200-43951400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr10:43950200-43951400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr10:43950200-43951400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:43950200-43951400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr10:43950200-43951400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:43950200-43951400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr10:43950200-43951400	Active TSS	Brain Germinal Matrix	brain
25	chr10:43950200-43951400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr10:43950200-43951400	Active TSS	Fetal Lung	lung
27	chr10:43950200-43951400	Active TSS	Left Ventricle	heart
28	chr10:43950200-43951400	Active TSS	Pancreas	Pancrea
29	chr10:43950200-43951400	Active TSS	Stomach Smooth Muscle	stomach
30	chr10:43950200-43951400	Active TSS	HSMM	muscle
31	chr10:43950200-43951400	Active TSS	NHLF	lung
32	chr10:43950200-43951600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr10:43950200-43951600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:43950200-43951600	Active TSS	Brain Angular Gyrus	brain
35	chr10:43950200-43951600	Active TSS	Colon Smooth Muscle	Colon
36	chr10:43950200-43951600	Active TSS	Fetal Heart	heart
37	chr10:43950200-43951600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr10:43950200-43951600	Active TSS	Rectal Smooth Muscle	rectum
39	chr10:43950200-43951800	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr10:43950200-43951800	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr10:43950200-43951800	Active TSS	Fetal Brain Female	brain
42	chr10:43950200-43951800	Active TSS	Psoas Muscle	Psoas
43	chr10:43950200-43952000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr10:43950200-43952200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr10:43950200-43952200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr10:43950400-43951000	Bivalent/Poised TSS	HepG2	liver
47	chr10:43950400-43951200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr10:43950400-43951400	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr10:43950400-43951400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr10:43950400-43951400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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