Variant report

Variant	rs4779862
Chromosome Location	chr15:31633161-31633162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31618754..31620549-chr15:31631588..31633647,2	K562	blood:
2	chr15:31618168..31621382-chr15:31631982..31634646,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169926	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1465778	0.81[GIH][hapmap]
rs2241779	0.87[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs28633674	0.84[AFR][1000 genomes]
rs4779517	0.86[AFR][1000 genomes]
rs4779861	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4779863	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4779864	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs56150535	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72722828	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72722839	0.82[EUR][1000 genomes]
rs73381286	0.81[AFR][1000 genomes]
rs8027539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
6	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS 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	46 gene(s)	inside rSNPs	diseases
8	nsv456747	chr15:31537496-31637996	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv568772	chr15:31537496-31637996	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv1839818	chr15:31594828-31637996	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1050482	chr15:31601016-31672921	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv1048082	chr15:31610245-31667000	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv1045944	chr15:31610245-31672921	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
15	nsv516681	chr15:31616674-31675453	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv903841	chr15:31616674-31697242	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
17	nsv903842	chr15:31621321-31697242	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
18	nsv456748	chr15:31621321-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
19	nsv568801	chr15:31621321-31697642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
20	nsv1052942	chr15:31624164-31653633	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv1810782	chr15:31633161-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4779862	KLF13	cis	cerebellum	SCAN
rs4779862	SNORD115-40	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31621600-31637200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:31621800-31636000	Enhancers	Small Intestine	intestine
3	chr15:31621800-31637600	Enhancers	Psoas Muscle	Psoas
4	chr15:31622000-31634600	Enhancers	Stomach Mucosa	stomach
5	chr15:31622000-31637600	Enhancers	Left Ventricle	heart
6	chr15:31622200-31633200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:31622600-31640200	Enhancers	Pancreas	Pancrea
8	chr15:31622800-31657400	Enhancers	Right Atrium	heart
9	chr15:31623400-31637200	Enhancers	Liver	Liver
10	chr15:31623800-31634600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:31624400-31634800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:31624400-31635200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr15:31625200-31649000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:31626000-31638400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:31626200-31633600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr15:31626400-31638400	Enhancers	Fetal Muscle Trunk	muscle
17	chr15:31626600-31638400	Genic enhancers	Fetal Thymus	thymus
18	chr15:31627000-31637600	Enhancers	Colon Smooth Muscle	Colon
19	chr15:31627200-31635000	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr15:31627200-31635200	Enhancers	Colonic Mucosa	Colon
21	chr15:31627200-31643000	Genic enhancers	Spleen	Spleen
22	chr15:31628200-31633600	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr15:31628200-31635200	Enhancers	Brain Germinal Matrix	brain
24	chr15:31629000-31638200	Enhancers	Fetal Brain Male	brain
25	chr15:31630600-31633800	Genic enhancers	Fetal Stomach	stomach
26	chr15:31630800-31633600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:31631000-31634400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr15:31631000-31635600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr15:31631200-31634200	Enhancers	Primary B cells from cord blood	blood
30	chr15:31631200-31634800	Genic enhancers	Primary T cells from cord blood	blood
31	chr15:31631200-31635400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:31631200-31635600	Strong transcription	Dnd41	blood
33	chr15:31631400-31633200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:31631400-31633800	Weak transcription	HUVEC	blood vessel
35	chr15:31631400-31634200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:31631400-31634600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:31631400-31635200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:31631400-31635400	Weak transcription	Hela-S3	cervix
39	chr15:31631400-31636200	Genic enhancers	Monocytes-CD14+_RO01746	blood
40	chr15:31631400-31644400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:31631400-31645000	Enhancers	Brain Substantia Nigra	brain
42	chr15:31631600-31634600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
43	chr15:31631600-31634800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr15:31631600-31634800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:31631600-31644600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:31631800-31634200	Weak transcription	Fetal Lung	lung
47	chr15:31631800-31634200	Genic enhancers	Right Ventricle	heart
48	chr15:31631800-31635400	Genic enhancers	Primary monocytes fromperipheralblood	blood
49	chr15:31631800-31635400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr15:31631800-31636200	Enhancers	Brain Anterior Caudate	brain

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