Variant report

Variant	rs6719900
Chromosome Location	chr2:46730140-46730141
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46721452..46724242-chr2:46727690..46730244,3	MCF-7	breast:
2	chr2:46728323..46730226-chr2:46842794..46844864,2	K562	blood:
3	chr2:46729419..46731731-chr2:46769469..46771571,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119729	Chromatin interaction
ENSG00000119878	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000151665	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1551123	0.81[CHD][hapmap]
rs1562454	0.81[CHD][hapmap]
rs17035200	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs55871716	0.83[ASN][1000 genomes]
rs6745531	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6749107	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	36 gene(s)	inside rSNPs	diseases
8	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1000129	chr2:46723102-46733814	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6719900	SOCS5	cis	multi-tissue	Pritchard
rs6719900	CRIPT	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46727600-46731400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:46727600-46732400	Weak transcription	HMEC	breast
3	chr2:46727600-46733000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:46727600-46733400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:46727600-46738200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:46727800-46730200	Weak transcription	Right Atrium	heart
7	chr2:46727800-46730400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:46727800-46730400	Weak transcription	Placenta	Placenta
9	chr2:46727800-46730400	Weak transcription	HSMMtube	muscle
10	chr2:46727800-46731600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:46727800-46732000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:46727800-46732200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:46727800-46732200	Weak transcription	NHEK	skin
14	chr2:46728000-46730200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:46728000-46731200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:46728000-46732200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:46728000-46733200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:46728200-46730400	Weak transcription	Fetal Heart	heart
19	chr2:46728200-46730800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:46728200-46732000	Weak transcription	K562	blood
21	chr2:46728400-46731800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:46728400-46733000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:46729000-46731200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr2:46729200-46730400	Enhancers	Fetal Intestine Large	intestine
25	chr2:46729200-46730600	Enhancers	Fetal Intestine Small	intestine
26	chr2:46729200-46731600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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