Variant report

Variant	rs17102061
Chromosome Location	chr1:46639966-46639967
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	JUN	chr1:46638774-46641517	K562	blood:	n/a	chr1:46640276-46640289 chr1:46639425-46639434 chr1:46639421-46639434
2	CEBPB	chr1:46639872-46640702	Hela-S3	cervix:	n/a	chr1:46640279-46640290
3	REST	chr1:46638677-46639973	H1-neurons	neurons:	n/a	chr1:46639593-46639606
4	MAX	chr1:46639877-46640697	Hela-S3	cervix:	n/a	chr1:46640279-46640288
5	POLR2A	chr1:46638844-46639973	H1-neurons	neurons:	n/a	n/a
6	SMC3	chr1:46639864-46640892	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46596732..46600061-chr1:46639198..46641036,3	K562	blood:
2	chr1:46638980..46642595-chr1:46645721..46649189,9	MCF-7	breast:
3	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
4	chr1:46639014..46640668-chr1:46643175..46645407,2	K562	blood:
5	chr1:45985928..45987580-chr1:46638994..46641452,2	K562	blood:
6	chr1:45985928..45987580-chr1:46638994..46641452,3	K562	blood:
7	chr1:46635707..46641847-chr1:46658318..46665376,6	K562	blood:
8	chr1:46638350..46640274-chr1:46653055..46655408,2	K562	blood:
9	chr1:46501684..46503933-chr1:46638611..46640285,2	K562	blood:
10	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:

Variant related genes	Relation type
TSPAN1	TF binding region
ENSG00000117461	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000227857	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11804982	1.00[MEX][hapmap]
rs12124649	1.00[JPT][hapmap]
rs17101983	1.00[MEX][hapmap]
rs1983261	1.00[MEX][hapmap]

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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46635600-46642200	Enhancers	Lung	lung
2	chr1:46636800-46641200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:46636800-46641400	Enhancers	Placenta	Placenta
4	chr1:46636800-46642200	Enhancers	Left Ventricle	heart
5	chr1:46636800-46642400	Enhancers	Right Atrium	heart
6	chr1:46636800-46642400	Enhancers	Right Ventricle	heart
7	chr1:46637000-46641200	Enhancers	Fetal Muscle Leg	muscle
8	chr1:46637800-46640400	Weak transcription	Small Intestine	intestine
9	chr1:46637800-46649600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:46638000-46640000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:46638000-46640600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:46638000-46645000	Weak transcription	HMEC	breast
13	chr1:46638600-46641400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:46638600-46641400	Enhancers	Fetal Heart	heart
15	chr1:46638800-46640000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:46638800-46640000	Bivalent Enhancer	HepG2	liver
17	chr1:46638800-46640000	Enhancers	HSMMtube	muscle
18	chr1:46638800-46640200	Enhancers	K562	blood
19	chr1:46638800-46640400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:46638800-46640800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:46638800-46640800	Enhancers	Osteobl	bone
22	chr1:46638800-46641000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:46638800-46641000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:46638800-46641000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:46638800-46641200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:46638800-46641200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:46639000-46640200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:46639000-46640400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:46639000-46640600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:46639000-46640600	Enhancers	Brain Hippocampus Middle	brain
31	chr1:46639000-46640600	Enhancers	Fetal Muscle Trunk	muscle
32	chr1:46639000-46640600	Enhancers	Fetal Stomach	stomach
33	chr1:46639000-46640800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr1:46639000-46640800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:46639000-46640800	Enhancers	NHDF-Ad	bronchial
36	chr1:46639000-46641000	Enhancers	H9 Cell Line	embryonic stem cell
37	chr1:46639000-46641000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:46639000-46641000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:46639000-46641000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:46639000-46641000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:46639000-46641000	Enhancers	Gastric	stomach
42	chr1:46639000-46641000	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr1:46639000-46641000	Enhancers	NHLF	lung
44	chr1:46639000-46641200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:46639000-46641200	Enhancers	Brain Substantia Nigra	brain
46	chr1:46639000-46641200	Enhancers	Fetal Thymus	thymus
47	chr1:46639000-46641200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:46639000-46641200	Enhancers	GM12878-XiMat	blood
49	chr1:46639000-46641400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:46639000-46641400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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