Variant report

Variant	rs9381884
Chromosome Location	chr6:13278788-13278789
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	chr6:13277312-13278911	GM12878	blood:	n/a	n/a
2	CTCF	chr6:13278436-13278843	GM12878	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
3	RAD21	chr6:13278434-13278871	ECC-1	luminal epithelium:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
4	POLR2A	chr6:13278014-13278909	GM12892	blood:	n/a	n/a
5	RAD21	chr6:13278368-13278844	H1-hESC	embryonic stem cell:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
6	RAD21	chr6:13278393-13278834	MCF-7	breast:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
7	CTCF	chr6:13278325-13278910	SK-N-SH	brain:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
8	SMC3	chr6:13278312-13278911	SK-N-SH	brain:	n/a	chr6:13278621-13278635
9	RAD21	chr6:13278381-13278845	H1-hESC	embryonic stem cell:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
10	CTCF	chr6:13278462-13278869	MCF-7	breast:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
11	RAD21	chr6:13278410-13278877	HepG2	liver:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
12	RAD21	chr6:13278421-13278829	H1-hESC	embryonic stem cell:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
13	POLR2A	chr6:13278150-13279049	K562	blood:	n/a	n/a
14	CTCF	chr6:13278660-13278810	GM12864	blood:	n/a	n/a
15	CTCF	chr6:13278358-13278909	MCF-7	breast:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
16	RAD21	chr6:13278429-13278933	SK-N-SH	brain:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
17	POLR2A	chr6:13277957-13284428	GM12878	blood:	n/a	n/a
18	SMC3	chr6:13278450-13278799	GM12878	blood:	n/a	chr6:13278621-13278635
19	BCLAF1	chr6:13278331-13278849	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:13278505-13278798	K562	blood:	n/a	n/a
21	CTCF	chr6:13278720-13278870	HFF	foreskin:	n/a	n/a
22	CTCF	chr6:13278509-13278804	K562	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
23	CTCF	chr6:13278640-13278790	NHDF-neo	bronchial:	n/a	n/a
24	POLR2A	chr6:13278316-13278832	GM12892	blood:	n/a	n/a
25	ZNF143	chr6:13278307-13278814	GM12878	blood:	n/a	n/a
26	RAD21	chr6:13278196-13278828	GM12878	blood:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
27	CTCF	chr6:13278435-13278831	HepG2	liver:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
28	CTCF	chr6:13278363-13278984	A549	lung:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
29	PML	chr6:13278351-13278843	GM12878	blood:	n/a	chr6:13278658-13278666
30	RAD21	chr6:13278434-13278807	GM12878	blood:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13266277..13270174-chr6:13278637..13282022,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215022	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1223397	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223399	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223400	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223401	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223402	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223403	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1232392	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13191897	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13205692	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17700321	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17767967	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202016	0.80[ASN][1000 genomes]
rs202017	0.80[ASN][1000 genomes]
rs202018	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs202019	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs202021	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs202023	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2048552	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs20499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs20500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439534	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439535	0.80[ASN][1000 genomes]
rs2439537	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439539	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439541	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439542	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439545	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439548	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439549	0.80[ASN][1000 genomes]
rs2458309	0.80[ASN][1000 genomes]
rs2458310	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2458311	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2458312	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2458314	0.81[JPT][hapmap]
rs2496140	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2496142	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2496144	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2496145	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2496147	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2496148	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2496149	0.80[ASN][1000 genomes]
rs2496151	0.80[ASN][1000 genomes]
rs2496152	0.80[ASN][1000 genomes]
rs2496153	0.80[ASN][1000 genomes]
rs2496154	0.80[ASN][1000 genomes]
rs2496156	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2496157	0.81[JPT][hapmap]
rs2919685	0.80[ASN][1000 genomes]
rs2919686	0.80[ASN][1000 genomes]
rs3001966	0.80[ASN][1000 genomes]
rs3001967	0.80[ASN][1000 genomes]
rs34505804	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35511719	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35549743	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3734878	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3817737	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817742	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402705	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs449727	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs452309	0.80[ASN][1000 genomes]
rs453877	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs617580	0.88[JPT][hapmap]
rs641758	0.81[JPT][hapmap]
rs9349564	0.80[ASN][1000 genomes]
rs9357660	0.83[ASN][1000 genomes]
rs9395602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957175	0.80[ASN][1000 genomes]
rs957176	0.80[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:80 , 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	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
4	chr6:13268000-13278800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
8	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:13270200-13291600	Weak transcription	HSMM	muscle
11	chr6:13270400-13282000	Weak transcription	Ovary	ovary
12	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
13	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
16	chr6:13273000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:13273400-13286800	Weak transcription	Liver	Liver
18	chr6:13273800-13279400	Weak transcription	Brain Angular Gyrus	brain
19	chr6:13273800-13280400	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
21	chr6:13274000-13282600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:13274000-13283800	Weak transcription	Brain Substantia Nigra	brain
23	chr6:13274400-13286800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:13274400-13287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
26	chr6:13274600-13279400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:13274600-13286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:13274600-13286800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
30	chr6:13274800-13286600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:13274800-13287000	Weak transcription	Thymus	Thymus
32	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:13275000-13280400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:13275000-13282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:13275000-13285000	Weak transcription	Fetal Intestine Small	intestine
36	chr6:13275000-13286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:13275000-13287000	Weak transcription	Gastric	stomach
38	chr6:13275200-13280200	Weak transcription	Primary T cells from cord blood	blood
39	chr6:13275200-13286400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:13275600-13280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:13275600-13281000	Weak transcription	Placenta	Placenta
42	chr6:13275600-13286600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:13275600-13287000	Weak transcription	Adipose Nuclei	Adipose
44	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:13275800-13282200	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:13276000-13279800	Weak transcription	Spleen	Spleen
47	chr6:13276000-13282800	Weak transcription	Right Ventricle	heart
48	chr6:13276000-13287400	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr6:13276200-13279600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr6:13276200-13281400	Genic enhancers	Primary B cells from cord blood	blood

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