Variant report

Variant	rs12530202
Chromosome Location	chr6:15247393-15247394
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	CEBPD	chr6:15246761-15247567	K562	blood:	n/a	n/a
2	SIN3AK20	chr6:15246875-15247463	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:15245216-15247511	GM12891	blood:	n/a	n/a
4	SIN3AK20	chr6:15246858-15247399	K562	blood:	n/a	n/a
5	PML	chr6:15245468-15247506	K562	blood:	n/a	n/a
6	NR2F2	chr6:15246711-15248457	K562	blood:	n/a	n/a
7	TEAD4	chr6:15246998-15247792	K562	blood:	n/a	n/a
8	ARID3A	chr6:15245618-15247596	K562	blood:	n/a	n/a
9	SMC3	chr6:15245077-15247478	Hela-S3	cervix:	n/a	chr6:15246683-15246691
10	RAD21	chr6:15244609-15249567	IMR90	lung:	n/a	chr6:15248721-15248734 chr6:15249188-15249197
11	IRF1	chr6:15246040-15248311	K562	blood:	n/a	chr6:15246366-15246380 chr6:15246928-15246942 chr6:15246535-15246551 chr6:15246364-15246384 chr6:15246366-15246376
12	GATA2	chr6:15246600-15248381	SH-SY5Y	brain:	n/a	chr6:15247976-15247983 chr6:15247972-15247988
13	GATA2	chr6:15246768-15248361	HUVEC	blood vessel:	n/a	chr6:15247976-15247983 chr6:15247972-15247988
14	RFX5	chr6:15246795-15247522	K562	blood:	n/a	n/a
15	CEBPB	chr6:15246561-15247462	Hela-S3	cervix:	n/a	chr6:15247202-15247214
16	HCFC1	chr6:15244775-15250295	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr6:15245570-15248437	PBDE	blood:	n/a	n/a
18	CHD1	chr6:15244739-15251552	IMR90	lung:	n/a	chr6:15245627-15245637 chr6:15245113-15245123
19	IRF1	chr6:15247301-15248309	K562	blood:	n/a	n/a
20	ZNF384	chr6:15245901-15248319	K562	blood:	n/a	n/a
21	GATA1	chr6:15245851-15248403	PBDE	blood:	n/a	chr6:15247976-15247983 chr6:15246000-15246008 chr6:15247972-15247988
22	MXI1	chr6:15243797-15248662	SK-N-SH	brain:	n/a	n/a
23	MXI1	chr6:15246857-15247835	Hela-S3	cervix:	n/a	n/a
24	UBTF	chr6:15247013-15247531	K562	blood:	n/a	n/a
25	MXI1	chr6:15244534-15249045	IMR90	lung:	n/a	n/a
26	POLR2A	chr6:15246634-15247509	K562	blood:	n/a	n/a
27	PML	chr6:15244952-15247474	K562	blood:	n/a	n/a
28	CEBPB	chr6:15246662-15247417	IMR90	lung:	n/a	chr6:15247202-15247214
29	MYC	chr6:15247191-15248141	MCF10A-Er-Src	breast:	n/a	n/a
30	TAF7	chr6:15247190-15248601	H1-hESC	embryonic stem cell:	n/a	n/a
31	STAT3	chr6:15247286-15247463	MCF10A-Er-Src	breast:	n/a	n/a
32	SIN3AK20	chr6:15245800-15247443	K562	blood:	n/a	n/a
33	TAL1	chr6:15246967-15247473	K562	blood:	n/a	n/a
34	MXI1	chr6:15244853-15247565	K562	blood:	n/a	n/a
35	RUNX3	chr6:15246637-15247765	GM12878	blood:	n/a	n/a
36	MYC	chr6:15244317-15247655	K562	blood:	n/a	chr6:15245090-15245099 chr6:15245854-15245864 chr6:15245068-15245078 chr6:15245035-15245044 chr6:15246339-15246347 chr6:15245866-15245875
37	POLR2A	chr6:15247045-15247427	MCF-7	breast:	n/a	n/a
38	TCF7L2	chr6:15246810-15248342	HEK293	kidney:	n/a	chr6:15247063-15247077 chr6:15247065-15247074
39	RFX5	chr6:15245108-15247458	Hela-S3	cervix:	n/a	chr6:15246220-15246229
40	MXI1	chr6:15246850-15247812	GM12878	blood:	n/a	n/a
41	TBP	chr6:15246790-15247443	K562	blood:	n/a	n/a
42	SIN3AK20	chr6:15244691-15247652	MCF-7	breast:	n/a	n/a
43	POLR2A	chr6:15244299-15251638	IMR90	lung:	n/a	n/a
44	CEBPB	chr6:15246548-15247477	K562	blood:	n/a	chr6:15247202-15247214
45	MAZ	chr6:15244502-15250215	IMR90	lung:	n/a	chr6:15245090-15245099 chr6:15245854-15245864 chr6:15245068-15245078 chr6:15245035-15245044 chr6:15246339-15246347 chr6:15245866-15245875
46	UBTF	chr6:15246673-15247581	K562	blood:	n/a	n/a
47	SREBP1	chr6:15245460-15248455	GM12878	blood:	n/a	chr6:15245880-15245890 chr6:15245881-15245892
48	SIN3A	chr6:15244262-15249916	H1-hESC	embryonic stem cell:	n/a	chr6:15245781-15245794 chr6:15245860-15245873 chr6:15246111-15246122 chr6:15248713-15248724
49	RAD21	chr6:15246993-15247509	H1-hESC	embryonic stem cell:	n/a	n/a
50	TBL1XR1	chr6:15246778-15247710	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:73159961..73161468-chr6:15245967..15247768,2	K562	blood:
2	chr6:14695043..14697656-chr6:15246930..15248844,2	K562	blood:
3	chr6:15246564..15248126-chr6:15304464..15306021,2	K562	blood:
4	chr6:15244134..15247491-chr6:15313536..15316337,3	K562	blood:
5	chr6:15085986..15094450-chr6:15243173..15249347,32	MCF-7	breast:
6	chr6:15238350..15240596-chr6:15246578..15248795,2	MCF-7	breast:
7	chr6:15088518..15090840-chr6:15243708..15248817,8	MCF-7	breast:
8	chr6:15087836..15090279-chr6:15247303..15249952,4	K562	blood:
9	chr6:15090854..15092609-chr6:15247191..15248815,2	MCF-7	breast:
10	chr6:15147856..15151805-chr6:15244004..15248641,4	MCF-7	breast:
11	chr6:15087697..15092455-chr6:15243972..15249952,11	K562	blood:

Variant related genes	Relation type
ENSG00000271888	TF binding region
JARID2	TF binding region
ENSG00000234261	Chromatin interaction
ENSG00000201367	Chromatin interaction
ENSG00000264687	Chromatin interaction
ENSG00000223247	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12524343	0.90[CEU][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12527989	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529516	1.00[ASN][1000 genomes]
rs12529596	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529633	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17687052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1969755	0.97[ASN][1000 genomes]
rs2295954	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34100628	0.82[ASN][1000 genomes]
rs58894024	0.82[ASN][1000 genomes]
rs59583140	0.82[ASN][1000 genomes]
rs59928045	0.82[ASN][1000 genomes]
rs6909967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73359662	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375535	0.82[ASN][1000 genomes]
rs73375542	0.82[ASN][1000 genomes]
rs73375558	0.82[ASN][1000 genomes]
rs73375561	0.82[ASN][1000 genomes]
rs73375565	0.90[ASN][1000 genomes]
rs7747401	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1818166	chr6:15247393-15250052	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 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	chr6:15243200-15248400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:15243600-15250200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:15243800-15248400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr6:15244000-15250000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:15244200-15249400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:15244200-15249800	Active TSS	Rectal Smooth Muscle	rectum
7	chr6:15244400-15247600	Active TSS	Primary T cells from cord blood	blood
8	chr6:15244400-15249200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:15244400-15249400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:15244400-15249600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr6:15244400-15250200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:15244400-15250400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:15244600-15247400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:15244600-15247600	Active TSS	Fetal Brain Female	brain
15	chr6:15244600-15248400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:15244600-15248400	Active TSS	NHDF-Ad	bronchial
17	chr6:15244600-15249200	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr6:15244600-15249200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:15244600-15249200	Active TSS	Duodenum Mucosa	Duodenum
20	chr6:15244600-15249200	Active TSS	NH-A	brain
21	chr6:15244600-15249200	Active TSS	Osteobl	bone
22	chr6:15244600-15249400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr6:15244600-15249400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr6:15244600-15249400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:15244600-15249400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:15244600-15249400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:15244600-15249400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:15244600-15249400	Active TSS	Brain Anterior Caudate	brain
29	chr6:15244600-15249400	Active TSS	Fetal Intestine Large	intestine
30	chr6:15244600-15249400	Active TSS	Thymus	Thymus
31	chr6:15244600-15249400	Active TSS	HSMM	muscle
32	chr6:15244600-15249600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:15244600-15249600	Active TSS	Brain Angular Gyrus	brain
34	chr6:15244600-15249600	Active TSS	Right Ventricle	heart
35	chr6:15244600-15249800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:15244600-15249800	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr6:15244600-15249800	Active TSS	Ovary	ovary
38	chr6:15244600-15249800	Active TSS	Psoas Muscle	Psoas
39	chr6:15244600-15250000	Active TSS	NHLF	lung
40	chr6:15244600-15250200	Active TSS	A549	lung
41	chr6:15244600-15250400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr6:15244800-15247400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:15244800-15247400	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr6:15244800-15249200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:15244800-15249200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr6:15244800-15249200	Active TSS	Left Ventricle	heart
47	chr6:15244800-15249200	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr6:15244800-15249400	Active TSS	Brain Substantia Nigra	brain
49	chr6:15244800-15249400	Active TSS	Fetal Kidney	kidney
50	chr6:15244800-15249400	Active TSS	Fetal Lung	lung

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