Variant report

Variant	rs701655
Chromosome Location	chr6:69942506-69942507
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	REST	chr6:69942404-69943313	HepG2	liver:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
2	REST	chr6:69942026-69943669	HL-60	blood:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
3	REST	chr6:69942500-69942684	HepG2	liver:	n/a	n/a
4	REST	chr6:69941912-69943831	H1-neurons	neurons:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
5	REST	chr6:69942438-69943264	GM12878	blood:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
6	TAF1	chr6:69942438-69943114	H1-neurons	neurons:	n/a	n/a
7	REST	chr6:69942308-69943416	PFSK-1	brain:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
8	REST	chr6:69942217-69943750	PANC-1	pancreas:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
9	REST	chr6:69942411-69943481	ECC-1	luminal epithelium:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
10	RAD21	chr6:69942464-69942669	SK-N-SH_RA	brain:	n/a	chr6:69942535-69942545
11	CTCF	chr6:69942480-69942630	BE2_C	brain:	n/a	n/a
12	CTCF	chr6:69942460-69942610	SK-N-SH_RA	brain:	n/a	n/a
13	GATA2	chr6:69941781-69943407	SH-SY5Y	brain:	n/a	chr6:69943061-69943071 chr6:69942181-69942191
14	REST	chr6:69942212-69943443	GM12878	blood:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
15	REST	chr6:69942297-69943463	PFSK-1	brain:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
16	RAD21	chr6:69942395-69942674	SK-N-SH_RA	brain:	n/a	chr6:69942535-69942545
17	CTCF	chr6:69942440-69942590	SK-N-SH_RA	brain:	n/a	n/a
18	RAD21	chr6:69942400-69943105	H1-hESC	embryonic stem cell:	n/a	chr6:69942535-69942545
19	REST	chr6:69942192-69943508	PFSK-1	brain:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
20	REST	chr6:69942397-69943483	ECC-1	luminal epithelium:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
21	REST	chr6:69942421-69943404	PANC-1	pancreas:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
22	REST	chr6:69942388-69943368	K562	blood:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
23	REST	chr6:69942460-69943359	A549	lung:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
24	CTCF	chr6:69942460-69942610	WERI-Rb-1	eye:	n/a	n/a
25	REST	chr6:69942391-69943445	HL-60	blood:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
26	POLR2A	chr6:69942001-69943491	H1-neurons	neurons:	n/a	n/a
27	REST	chr6:69942410-69943257	H1-neurons	neurons:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
28	REST	chr6:69942413-69942660	SK-N-SH	brain:	n/a	n/a
29	MXI1	chr6:69942173-69943411	IMR90	lung:	n/a	n/a
30	REST	chr6:69942409-69943419	MCF-7	breast:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
31	REST	chr6:69942413-69943367	SK-N-SH	brain:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
32	MXI1	chr6:69940711-69943670	SK-N-SH	brain:	n/a	n/a
33	REST	chr6:69942339-69943461	H1-hESC	embryonic stem cell:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
34	REST	chr6:69942402-69943533	PANC-1	pancreas:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
35	REST	chr6:69942375-69943401	H1-hESC	embryonic stem cell:	n/a	chr6:69942876-69942894 chr6:69942953-69942962 chr6:69942935-69942949 chr6:69942972-69942985
36	POLR2A	chr6:69942362-69943502	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
BAI3	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11962594	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11965487	1.00[CEU][hapmap]
rs1283464	1.00[CEU][hapmap]
rs1293154	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1297415	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13195278	1.00[CEU][hapmap]
rs1410699	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1512234	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16900620	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1706838	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1928060	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs314208	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs314216	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs35829738	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6919623	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs701656	0.89[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71557617	0.92[EUR][1000 genomes]
rs728299	0.92[AFR][1000 genomes]
rs7751967	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs779455	0.90[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs779459	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs779461	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs779462	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs779464	0.87[YRI][hapmap]
rs779467	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs779470	0.90[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs779474	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs779483	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs779487	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs779492	0.86[EUR][1000 genomes]
rs9346271	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886137	chr6:69684850-70095690	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv432919	chr6:69873179-70221322	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69941600-69943000	Weak transcription	Fetal Lung	lung
2	chr6:69941800-69942600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:69941800-69943000	Weak transcription	Fetal Kidney	kidney
4	chr6:69942000-69942600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr6:69942200-69942600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
6	chr6:69942200-69942600	Flanking Active TSS	Fetal Brain Male	brain
7	chr6:69942200-69942600	Flanking Active TSS	Fetal Brain Female	brain
8	chr6:69942200-69942800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:69942200-69944000	Active TSS	Brain Germinal Matrix	brain
10	chr6:69942200-69945200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:69942200-69946200	Active TSS	Brain Anterior Caudate	brain
12	chr6:69942400-69942600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr6:69942400-69942600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:69942400-69942600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr6:69942400-69942600	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:69942400-69942600	Enhancers	Brain Hippocampus Middle	brain
17	chr6:69942400-69942800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
18	chr6:69942400-69942800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
19	chr6:69942400-69943000	Enhancers	H9 Cell Line	embryonic stem cell
20	chr6:69942400-69943000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:69942400-69943200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr6:69942400-69943200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:69942400-69943400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr6:69942400-69943400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr6:69942400-69943600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:69942400-69943600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:69942400-69943600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:69942400-69944800	Active TSS	Brain Cingulate Gyrus	brain
29	chr6:69942400-69945000	Active TSS	Brain Angular Gyrus	brain
30	chr6:69942400-69945600	Active TSS	Brain Inferior Temporal Lobe	brain

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