Variant report

Variant	rs202045
Chromosome Location	chr6:13275914-13275915
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:13275900-13276050	K562	blood:	n/a	n/a
2	RUNX3	chr6:13275445-13276035	GM12878	blood:	n/a	n/a
3	USF2	chr6:13275890-13275985	GM12878	blood:	n/a	n/a
4	MAZ	chr6:13275435-13276088	K562	blood:	n/a	n/a
5	TBL1XR1	chr6:13275825-13276122	K562	blood:	n/a	n/a
6	HMGN3	chr6:13275359-13275993	K562	blood:	n/a	n/a
7	SMC3	chr6:13275868-13276192	GM12878	blood:	n/a	n/a
8	RCOR1	chr6:13275515-13276686	K562	blood:	n/a	n/a
9	POLR2A	chr6:13275249-13276119	K562	blood:	n/a	n/a
10	NR2F2	chr6:13275821-13276756	K562	blood:	n/a	n/a
11	HCFC1	chr6:13275447-13276115	K562	blood:	n/a	n/a
12	CTCF	chr6:13275837-13276178	K562	blood:	n/a	n/a
13	POLR2A	chr6:13275519-13275928	GM12891	blood:	n/a	n/a
14	POLR2A	chr6:13275332-13276102	K562	blood:	n/a	n/a
15	CEBPB	chr6:13275383-13276046	K562	blood:	n/a	n/a
16	ATF2	chr6:13275293-13276112	GM12878	blood:	n/a	n/a
17	ZC3H11A	chr6:13275426-13275928	K562	blood:	n/a	n/a
18	JUN	chr6:13272018-13276804	K562	blood:	n/a	chr6:13276647-13276657
19	RELA	chr6:13272415-13276072	GM10847	blood:	n/a	n/a
20	MXI1	chr6:13275628-13276307	GM12878	blood:	n/a	n/a
21	CTCF	chr6:13275806-13276209	K562	blood:	n/a	n/a
22	POLR2A	chr6:13272223-13276600	GM12878	blood:	n/a	n/a
23	NR2F2	chr6:13272645-13276785	K562	blood:	n/a	n/a
24	MAX	chr6:13275287-13276147	K562	blood:	n/a	n/a
25	POLR2A	chr6:13275219-13276292	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:13272237-13275957	GM12892	blood:	n/a	n/a
27	CREB1	chr6:13275308-13276029	GM12878	blood:	n/a	n/a
28	CTCF	chr6:13275900-13276050	HepG2	liver:	n/a	n/a
29	MAFK	chr6:13275435-13276639	K562	blood:	n/a	n/a
30	E2F6	chr6:13275663-13276046	K562	blood:	n/a	n/a
31	MAX	chr6:13275613-13276055	K562	blood:	n/a	n/a
32	POLR2A	chr6:13275817-13275961	GM12878	blood:	n/a	n/a
33	BHLHE40	chr6:13275557-13275961	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:13271496-13276674	K562	blood:	n/a	n/a
35	ZNF384	chr6:13275392-13276623	K562	blood:	n/a	n/a
36	POLR2A	chr6:13272368-13276162	GM12878	blood:	n/a	n/a
37	MTA3	chr6:13272032-13276170	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:13275242-13276010	GM12892	blood:	n/a	n/a
39	MAFF	chr6:13275616-13276591	K562	blood:	n/a	n/a
40	CTCF	chr6:13275859-13276193	GM12878	blood:	n/a	n/a
41	RAD21	chr6:13275856-13276217	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr6:13275231-13276112	GM12892	blood:	n/a	n/a
43	TEAD4	chr6:13275560-13276801	K562	blood:	n/a	n/a
44	CBX3	chr6:13275271-13276781	K562	blood:	n/a	n/a
45	MYC	chr6:13275451-13276633	K562	blood:	n/a	n/a
46	ZNF143	chr6:13275838-13276176	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:13275246-13276072	GM12891	blood:	n/a	n/a
48	WRNIP1	chr6:13275322-13276146	GM12878	blood:	n/a	n/a
49	CHD1	chr6:13272315-13276002	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:13272116-13276591	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13268970..13278598-chr6:13326296..13332818,15	K562	blood:
2	chr6:13274897..13277892-chr6:13326296..13329891,5	K562	blood:
3	chr6:13273285..13276286-chr6:13486162..13489029,4	K562	blood:
4	chr6:13273285..13276286-chr6:13486162..13489029,3	K562	blood:
5	chr6:13274197..13275936-chr6:13573987..13576342,2	K562	blood:
6	chr6:13246618..13250195-chr6:13274363..13276198,3	K562	blood:
7	chr6:13274736..13276491-chr6:13282500..13284996,2	MCF-7	breast:

No data

Variant related genes	Relation type
PHACTR1	TF binding region
ENSG00000215022	TF binding region
ENSG00000187461	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000215022	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1512414	0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1550526	0.81[CEU][hapmap]
rs2002961	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs202028	0.80[ASN][1000 genomes]
rs202030	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs202034	0.81[ASN][1000 genomes]
rs202038	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs202040	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs202042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202046	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202048	0.82[ASN][1000 genomes]
rs202051	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs202053	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs202070	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs202071	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs202072	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs202073	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs202077	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2119485	0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs375661	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs3817735	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs384730	0.86[YRI][hapmap]
rs3857594	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs405078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs412787	0.86[YRI][hapmap]
rs413120	1.00[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs441213	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs442614	0.86[YRI][hapmap]
rs445591	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs445714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs454563	0.81[CEU][hapmap]
rs4602719	0.81[CEU][hapmap]
rs475165	0.85[ASN][1000 genomes]
rs495895	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6909879	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6922200	0.85[ASN][1000 genomes]
rs6923757	0.85[ASN][1000 genomes]
rs6924855	0.85[ASN][1000 genomes]
rs7755309	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs8541	0.81[CEU][hapmap]
rs878700	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs909508	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9296641	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9296642	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9349548	0.83[ASN][1000 genomes]
rs9349549	0.81[ASN][1000 genomes]
rs9369976	0.85[ASN][1000 genomes]
rs9369978	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9369979	0.85[ASN][1000 genomes]
rs9473908	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9473909	0.94[JPT][hapmap];0.85[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer 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	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
2	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
3	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
5	chr6:13268000-13278800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
9	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:13270200-13291600	Weak transcription	HSMM	muscle
12	chr6:13270400-13282000	Weak transcription	Ovary	ovary
13	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
14	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
17	chr6:13272200-13276200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr6:13272400-13276600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:13273000-13277200	Weak transcription	Lung	lung
20	chr6:13273000-13277800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:13273000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:13273200-13277200	Weak transcription	Left Ventricle	heart
23	chr6:13273400-13286800	Weak transcription	Liver	Liver
24	chr6:13273600-13277600	Weak transcription	Fetal Stomach	stomach
25	chr6:13273800-13277400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:13273800-13277400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:13273800-13279400	Weak transcription	Brain Angular Gyrus	brain
28	chr6:13273800-13280400	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
30	chr6:13274000-13277800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:13274000-13282600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:13274000-13283800	Weak transcription	Brain Substantia Nigra	brain
33	chr6:13274200-13276600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:13274400-13276400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:13274400-13277400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:13274400-13277600	Weak transcription	Brain Anterior Caudate	brain
37	chr6:13274400-13286800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:13274400-13287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
40	chr6:13274600-13279400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:13274600-13286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:13274600-13286800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
44	chr6:13274800-13277600	Weak transcription	Aorta	Aorta
45	chr6:13274800-13278000	Weak transcription	Fetal Thymus	thymus
46	chr6:13274800-13286600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:13274800-13287000	Weak transcription	Thymus	Thymus
48	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:13275000-13276400	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr6:13275000-13276800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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