Variant report

Variant	rs4993742
Chromosome Location	chr1:223841341-223841342
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223833118..223836523-chr1:223838327..223841763,4	MCF-7	breast:
2	chr1:223840282..223843675-chr1:223851675..223856291,7	MCF-7	breast:
3	chr1:223840874..223841758-chr8:63546888..63547676,2	MCF-7	breast:
4	chr1:223834427..223836360-chr1:223837595..223841642,3	MCF-7	breast:
5	chr1:223827148..223829506-chr1:223840054..223841666,2	MCF-7	breast:
6	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203697	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10465524	0.82[CEU][hapmap]
rs10495215	0.82[CEU][hapmap]
rs10495216	0.82[CEU][hapmap]
rs10495217	0.82[CEU][hapmap]
rs10503144	0.82[CEU][hapmap]
rs12059770	0.82[CEU][hapmap]
rs12080250	0.82[CEU][hapmap]
rs12088254	0.82[CEU][hapmap]
rs12563637	0.82[CEU][hapmap]
rs12565967	0.82[CEU][hapmap]
rs12566817	0.82[CEU][hapmap]
rs16842162	0.82[CEU][hapmap]
rs16842257	0.82[CEU][hapmap]
rs17557288	0.82[CEU][hapmap]
rs17557525	0.82[CEU][hapmap]
rs6604724	0.82[CEU][hapmap]
rs6678365	0.82[CEU][hapmap]
rs6685475	0.82[CEU][hapmap]
rs6685557	0.82[CEU][hapmap]
rs6691315	0.82[CEU][hapmap]
rs6693372	0.82[CEU][hapmap]
rs6693884	1.00[CEU][hapmap]
rs6694960	0.82[CEU][hapmap]
rs6696053	0.82[CEU][hapmap]
rs6700366	0.82[CEU][hapmap]
rs7331	0.82[CEU][hapmap]
rs7530328	0.82[CEU][hapmap]
rs7533551	0.82[CEU][hapmap]
rs7549063	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873209	chr1:223707647-223846564	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873212	chr1:223807262-223853792	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1012050	chr1:223824652-223843610	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv535309	chr1:223824652-223843610	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223830400-223841800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:223833600-223850800	Weak transcription	Colonic Mucosa	Colon
3	chr1:223834200-223841800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:223834400-223841600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:223838200-223841400	Enhancers	Fetal Muscle Leg	muscle
6	chr1:223838200-223842600	Weak transcription	Lung	lung
7	chr1:223838200-223850800	Weak transcription	Fetal Stomach	stomach
8	chr1:223839200-223841800	Enhancers	Fetal Brain Male	brain
9	chr1:223839200-223843600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:223839400-223841400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:223839600-223841600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:223839600-223841600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:223839600-223841800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:223839600-223843000	Weak transcription	Fetal Intestine Large	intestine
15	chr1:223839800-223841400	Enhancers	Fetal Thymus	thymus
16	chr1:223840000-223841600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:223840000-223843600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:223840200-223841400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:223840200-223841400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr1:223840200-223841400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:223840200-223841800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:223840600-223841800	Weak transcription	Esophagus	oesophagus
23	chr1:223840600-223843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:223840600-223843400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:223840600-223853200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:223840800-223841400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:223840800-223841800	Weak transcription	Fetal Lung	lung
28	chr1:223840800-223841800	Weak transcription	Psoas Muscle	Psoas
29	chr1:223840800-223843400	Enhancers	NHEK	skin
30	chr1:223840800-223843600	Enhancers	Stomach Mucosa	stomach
31	chr1:223841000-223841800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:223841000-223842000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:223841000-223842000	Weak transcription	Gastric	stomach
34	chr1:223841000-223842800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:223841000-223843000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:223841000-223843800	Enhancers	HMEC	breast
37	chr1:223841200-223841600	Enhancers	Brain Germinal Matrix	brain
38	chr1:223841200-223841600	Enhancers	A549	lung
39	chr1:223841200-223841800	Enhancers	Fetal Brain Female	brain

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