Variant report

Variant	rs16977644
Chromosome Location	chr15:58004888-58004889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58003308..58005192-chr15:58018137..58020325,2	MCF-7	breast:
2	chr15:57847110..57848744-chr15:58003353..58005954,2	K562	blood:
3	chr15:57957979..57959871-chr15:58003465..58005638,2	K562	blood:

Variant related genes	Relation type
ENSG00000240874	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1000697	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[ASN][1000 genomes]
rs1062707	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638075	0.96[ASN][1000 genomes]
rs1808478	0.83[ASW][hapmap];0.81[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2470361	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2733616	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2733617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2733619	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28489309	0.92[ASN][1000 genomes]
rs57986545	0.93[ASN][1000 genomes]
rs7178647	0.92[ASN][1000 genomes]
rs7181586	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs72745574	0.93[ASN][1000 genomes]
rs72745581	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16977644	SUV39H2	trans	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57999800-58008200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:57999800-58014400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:57999800-58022400	Weak transcription	Esophagus	oesophagus
4	chr15:58000000-58008200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:58000200-58015000	Weak transcription	Stomach Mucosa	stomach
6	chr15:58000800-58007000	Strong transcription	HSMM	muscle
7	chr15:58000800-58011400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:58000800-58012200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:58000800-58012800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:58001000-58006800	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr15:58001000-58007800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:58001000-58008600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:58001200-58006800	Strong transcription	Fetal Stomach	stomach
14	chr15:58001200-58006800	Strong transcription	NHDF-Ad	bronchial
15	chr15:58001200-58007000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr15:58001200-58007000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:58001200-58007000	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr15:58001200-58007600	Strong transcription	Osteobl	bone
19	chr15:58001200-58007800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:58001200-58007800	Strong transcription	A549	lung
21	chr15:58001200-58010200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:58001400-58005400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:58001400-58006800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:58001400-58006800	Strong transcription	Brain Angular Gyrus	brain
25	chr15:58001400-58006800	Strong transcription	NHLF	lung
26	chr15:58001400-58007000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:58001400-58007000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr15:58001400-58007400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:58001400-58007600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:58001400-58007600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr15:58001400-58007600	Strong transcription	HMEC	breast
32	chr15:58001400-58007800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:58001400-58007800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:58001400-58007800	Strong transcription	Brain Anterior Caudate	brain
35	chr15:58001400-58008000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:58001400-58008000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr15:58001400-58008000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr15:58001400-58008400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr15:58001400-58012800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:58001400-58013000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:58001600-58005400	Strong transcription	Brain Germinal Matrix	brain
42	chr15:58001600-58006800	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr15:58001600-58006800	Strong transcription	NH-A	brain
44	chr15:58001600-58007000	Strong transcription	HSMMtube	muscle
45	chr15:58001600-58007600	Strong transcription	Primary B cells from cord blood	blood
46	chr15:58001600-58007600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:58001600-58007600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:58001600-58007800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:58001600-58007800	Strong transcription	HUVEC	blood vessel
50	chr15:58001600-58008200	Strong transcription	Placenta	Placenta

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