Variant report

Variant	rs3817735
Chromosome Location	chr6:13278648-13278649
allele	A/G
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	CTCF	chr6:13278580-13278730	GM12872	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
2	CTCF	chr6:13278560-13278710	HepG2	liver:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
3	CTCF	chr6:13278502-13278763	GM19238	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
4	CTCF	chr6:13278540-13278690	GM12864	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
5	CTCF	chr6:13278514-13278760	GM12878	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
6	CTCF	chr6:13278555-13278662	ProgFib	skin:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
7	POLR2A	chr6:13277312-13278911	GM12878	blood:	n/a	n/a
8	CTCF	chr6:13278436-13278843	GM12878	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
9	CTCF	chr6:13278492-13278759	GM12891	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
10	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
11	CTCF	chr6:13278540-13278690	SAEC	small airway:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
12	CTCF	chr6:13278587-13278679	GM13976	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
13	ZNF384	chr6:13278003-13278720	GM12878	blood:	n/a	n/a
14	CTCF	chr6:13278520-13278670	GM12873	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
15	CTCF	chr6:13278620-13278770	AG09319	gingival:	n/a	chr6:13278621-13278634
16	POLR2A	chr6:13278604-13278662	K562	blood:	n/a	n/a
17	RAD21	chr6:13278439-13278768	HepG2	liver:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
18	CTCF	chr6:13278528-13278734	NHEK	skin:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
19	CTCF	chr6:13278538-13278750	LNCaP	prostate:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
20	CTCF	chr6:13278412-13278777	H1-hESC	embryonic stem cell:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
21	POLR2A	chr6:13278014-13278909	GM12892	blood:	n/a	n/a
22	CTCF	chr6:13278560-13278710	GM12869	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
23	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
24	RAD21	chr6:13278321-13278785	MCF-7	breast:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
25	CTCF	chr6:13278505-13278755	GM12892	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
26	CTCF	chr6:13278512-13278750	GM19240	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
27	CTCF	chr6:13278560-13278710	HCM	heart:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
28	CTCF	chr6:13278580-13278730	GM12867	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
29	CTCF	chr6:13278533-13278736	Hela-S3	cervix:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
30	CTCF	chr6:13278520-13278670	BJ	skin:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
31	ZNF143	chr6:13278476-13278784	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr6:13278540-13278690	GM12867	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
33	CTCF	chr6:13278560-13278710	BE2_C	brain:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
34	CTCF	chr6:13278560-13278710	HEK293	kidney:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
35	RAD21	chr6:13278393-13278834	MCF-7	breast:	n/a	chr6:13278621-13278631 chr6:13278621-13278635 chr6:13278620-13278633 chr6:13278619-13278631 chr6:13278617-13278636
36	CTCF	chr6:13278520-13278670	HPAF	blood vessel:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
37	CTCF	chr6:13278510-13278755	MCF-7	breast:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
38	CTCF	chr6:13278540-13278690	NB4	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
39	CTCF	chr6:13278590-13278753	LNCaP	prostate:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
40	CTCF	chr6:13278540-13278690	HRPEpiC	eye:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
41	CTCF	chr6:13278325-13278910	SK-N-SH	brain:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
42	CTCF	chr6:13278464-13278777	K562	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
43	CTCF	chr6:13278560-13278710	SAEC	small airway:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
44	CTCF	chr6:13278540-13278690	WERI-Rb-1	eye:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
45	MXI1	chr6:13278516-13278713	H1-hESC	embryonic stem cell:	n/a	n/a
46	SMC3	chr6:13278312-13278911	SK-N-SH	brain:	n/a	chr6:13278621-13278635
47	CTCF	chr6:13278510-13278760	GM19239	blood:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
48	CTCF	chr6:13278580-13278730	RPTEC	kidney:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
49	CTCF	chr6:13278530-13278740	Fibrobl	skin:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635
50	CTCF	chr6:13278540-13278690	HEK293	kidney:	n/a	chr6:13278621-13278634 chr6:13278619-13278637 chr6:13278614-13278635

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13274000..13275754-chr6:13276034..13278687,2	MCF-7	breast:
2	chr6:13266277..13270174-chr6:13278637..13282022,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215022	TF binding region
ENSG00000215022	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1150623	0.80[EUR][1000 genomes]
rs1223398	0.82[EUR][1000 genomes]
rs1512414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2002961	0.90[JPT][hapmap]
rs202042	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs202044	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs202045	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs202046	0.84[ASN][1000 genomes]
rs202051	0.95[JPT][hapmap]
rs202053	0.84[JPT][hapmap]
rs2119485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235173	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34148691	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs375661	0.87[ASN][1000 genomes]
rs377704	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3857594	0.90[JPT][hapmap]
rs405078	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs441213	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs445714	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs495895	0.87[ASN][1000 genomes]
rs6909879	0.90[JPT][hapmap]
rs7755309	0.90[JPT][hapmap]
rs878700	0.90[JPT][hapmap]
rs909508	0.90[JPT][hapmap]
rs9296641	0.90[JPT][hapmap]
rs9296642	0.90[JPT][hapmap]
rs9349548	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9349549	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9369978	0.90[JPT][hapmap]
rs9473908	0.89[JPT][hapmap]
rs9473909	0.90[JPT][hapmap]

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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