Variant report

Variant	rs6686661
Chromosome Location	chr1:46638537-46638538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr1:46636699-46638570	ECC-1	luminal epithelium:	n/a	chr1:46637847-46637856 chr1:46637179-46637186
2	CEBPB	chr1:46638536-46638773	IMR90	lung:	n/a	chr1:46638615-46638626
3	TCF12	chr1:46637356-46638706	MCF-7	breast:	n/a	n/a
4	TCF12	chr1:46636845-46638556	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
2	chr1:46636993..46639249-chr1:46644481..46646542,2	MCF-7	breast:
3	chr1:46636697..46639165-chr1:46652056..46653716,2	MCF-7	breast:
4	chr1:46635707..46641847-chr1:46658318..46665376,6	K562	blood:
5	chr1:46546706..46549522-chr1:46637741..46639306,2	MCF-7	breast:
6	chr1:46638350..46640274-chr1:46653055..46655408,2	K562	blood:
7	chr1:46501344..46502975-chr1:46637425..46639494,2	MCF-7	breast:
8	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
9	chr1:46630846..46632404-chr1:46635981..46638710,2	K562	blood:

No data

Variant related genes	Relation type
TSPAN1	TF binding region
ENSG00000227857	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000117461	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11211259	0.82[ASN][1000 genomes]
rs12029134	0.97[ASN][1000 genomes]
rs12029936	0.82[ASN][1000 genomes]
rs12134419	0.82[ASN][1000 genomes]
rs3845300	0.82[ASN][1000 genomes]
rs3845301	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3855959	0.80[ASN][1000 genomes]
rs7512966	0.94[ASN][1000 genomes]
rs7536272	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46633400-46638800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:46633400-46638800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:46633400-46638800	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:46633400-46638800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:46633600-46639200	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:46634400-46638800	Weak transcription	K562	blood
7	chr1:46635600-46642200	Enhancers	Lung	lung
8	chr1:46636800-46639400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr1:46636800-46641200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:46636800-46641400	Enhancers	Placenta	Placenta
11	chr1:46636800-46642200	Enhancers	Left Ventricle	heart
12	chr1:46636800-46642400	Enhancers	Right Atrium	heart
13	chr1:46636800-46642400	Enhancers	Right Ventricle	heart
14	chr1:46637000-46638600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:46637000-46641200	Enhancers	Fetal Muscle Leg	muscle
16	chr1:46637200-46639800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:46637400-46638800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:46637400-46638800	Weak transcription	Osteobl	bone
19	chr1:46637400-46639000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:46637400-46639000	Weak transcription	GM12878-XiMat	blood
21	chr1:46637400-46639200	Weak transcription	HSMM	muscle
22	chr1:46637600-46639000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:46637800-46638800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:46637800-46638800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:46637800-46638800	Enhancers	Hela-S3	cervix
26	chr1:46637800-46639000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:46637800-46639000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:46637800-46639000	Weak transcription	Fetal Thymus	thymus
29	chr1:46637800-46639400	Enhancers	Adipose Nuclei	Adipose
30	chr1:46637800-46639400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:46637800-46639600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:46637800-46640400	Weak transcription	Small Intestine	intestine
33	chr1:46637800-46649600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:46638000-46638800	Weak transcription	Brain Angular Gyrus	brain
35	chr1:46638000-46639000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:46638000-46639000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:46638000-46639000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:46638000-46639000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:46638000-46639000	Weak transcription	Fetal Lung	lung
40	chr1:46638000-46639000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:46638000-46639000	Weak transcription	Gastric	stomach
42	chr1:46638000-46639000	Weak transcription	Psoas Muscle	Psoas
43	chr1:46638000-46639000	Weak transcription	Spleen	Spleen
44	chr1:46638000-46639200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:46638000-46639200	Weak transcription	Colonic Mucosa	Colon
46	chr1:46638000-46639200	Weak transcription	Esophagus	oesophagus
47	chr1:46638000-46639200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:46638000-46639400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:46638000-46639800	Weak transcription	Stomach Mucosa	stomach
50	chr1:46638000-46639800	Weak transcription	NHEK	skin

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