Variant report

Variant	rs4779868
Chromosome Location	chr15:31654283-31654284
allele	A/G
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	GABPA	chr15:31653988-31654362	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr15:31653037-31654364	NB4	blood:	n/a	chr15:31654094-31654104 chr15:31653861-31653871
3	POLR2A	chr15:31652887-31654641	GM12878	blood:	n/a	n/a
4	MAX	chr15:31653949-31654326	K562	blood:	n/a	chr15:31654094-31654104
5	CREB1	chr15:31653331-31654298	GM12878	blood:	n/a	n/a
6	TAF1	chr15:31654119-31654328	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr15:31653237-31654591	NB4	blood:	n/a	chr15:31654094-31654104 chr15:31653861-31653871
8	MYC	chr15:31653860-31654565	K562	blood:	n/a	chr15:31654094-31654104 chr15:31653861-31653871
9	CTCF	chr15:31654160-31654310	HCM	heart:	n/a	n/a
10	GABPA	chr15:31653920-31654391	A549	lung:	n/a	n/a
11	CTCF	chr15:31654200-31654350	HRPEpiC	eye:	n/a	n/a
12	CTCF	chr15:31654140-31654290	SK-N-SH_RA	brain:	n/a	n/a
13	GABPA	chr15:31653942-31654346	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr15:31654180-31654330	GM12875	blood:	n/a	n/a
15	GABPA	chr15:31653487-31654386	HL-60	blood:	n/a	n/a
16	GABPA	chr15:31653927-31654389	MCF-7	breast:	n/a	n/a
17	MTA3	chr15:31653157-31654294	GM12878	blood:	n/a	n/a
18	GABPA	chr15:31653983-31654380	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr15:31653062-31654382	GM18951	blood:	n/a	n/a
20	POLR2A	chr15:31653334-31654441	HL-60	blood:	n/a	n/a
21	POLR2A	chr15:31653290-31654631	GM12878	blood:	n/a	n/a
22	CTCF	chr15:31654240-31654390	HAc	cerebellar:	n/a	n/a
23	CTCF	chr15:31654140-31654290	BE2_C	brain:	n/a	n/a
24	USF2	chr15:31653945-31654300	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr15:31653069-31654433	GM18505	blood:	n/a	n/a
26	SPI1	chr15:31653331-31654349	HL-60	blood:	n/a	chr15:31653812-31653825 chr15:31653816-31653823 chr15:31653812-31653825 chr15:31653815-31653824 chr15:31653813-31653826 chr15:31653474-31653487 chr15:31653766-31653779
27	TBP	chr15:31654042-31654350	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr15:31654160-31654310	HMF	breast:	n/a	n/a
29	CTCF	chr15:31654240-31654390	BE2_C	brain:	n/a	n/a
30	GABPA	chr15:31653891-31654367	A549	lung:	n/a	n/a
31	MAX	chr15:31653908-31654365	H1-hESC	embryonic stem cell:	n/a	chr15:31654094-31654104
32	RUNX3	chr15:31653181-31654284	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:31653098-31654482	GM12892	blood:	n/a	n/a
34	POLR2A	chr15:31653050-31654414	GM15510	blood:	n/a	n/a
35	SPI1	chr15:31653425-31654339	GM12878	blood:	n/a	chr15:31653812-31653825 chr15:31653816-31653823 chr15:31653812-31653825 chr15:31653815-31653824 chr15:31653813-31653826 chr15:31653474-31653487 chr15:31653766-31653779
36	CTCF	chr15:31654180-31654330	HVMF	connective:	n/a	n/a
37	POLR2A	chr15:31651668-31654442	GM12878	blood:	n/a	n/a
38	CTCF	chr15:31654240-31654390	GM12873	blood:	n/a	n/a
39	CTCF	chr15:31654184-31654292	H1-hESC	embryonic stem cell:	n/a	n/a
40	GABPA	chr15:31653991-31654328	H1-hESC	embryonic stem cell:	n/a	n/a
41	GABPA	chr15:31653400-31654485	HL-60	blood:	n/a	n/a
42	CTCF	chr15:31654200-31654350	HEK293	kidney:	n/a	n/a
43	POLR2A	chr15:31653118-31654446	HL-60	blood:	n/a	n/a
44	CTCF	chr15:31654140-31654290	HPAF	blood vessel:	n/a	n/a
45	POLR2A	chr15:31650909-31655557	GM12891	blood:	n/a	n/a
46	CTCF	chr15:31654200-31654350	AoAF	blood vessel:	n/a	n/a
47	HCFC1	chr15:31653970-31654311	K562	blood:	n/a	n/a
48	CTCF	chr15:31654140-31654290	GM12864	blood:	n/a	n/a
49	CTCF	chr15:31654140-31654290	GM12873	blood:	n/a	n/a
50	MAX	chr15:31653887-31654362	H1-hESC	embryonic stem cell:	n/a	chr15:31654094-31654104

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31653647..31656481-chr15:31658633..31661185,3	MCF-7	breast:
2	chr15:31647650..31653294-chr15:31653476..31658122,6	K562	blood:

Variant related genes	Relation type
KLF13	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12592176	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592541	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13329095	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13329369	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1807100	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961706	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241779	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28490143	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28633674	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28705115	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4779517	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4779518	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779863	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4779864	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56150535	0.85[AFR][1000 genomes]
rs7169662	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7174079	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755282	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8036899	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv1051910	chr15:31641254-31672921	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31622800-31657400	Enhancers	Right Atrium	heart
2	chr15:31638400-31655400	Enhancers	Psoas Muscle	Psoas
3	chr15:31641000-31655600	Enhancers	Left Ventricle	heart
4	chr15:31641200-31658400	Enhancers	Liver	Liver
5	chr15:31646000-31655200	Weak transcription	A549	lung
6	chr15:31646000-31659800	Weak transcription	Fetal Kidney	kidney
7	chr15:31646200-31655600	Enhancers	Right Ventricle	heart
8	chr15:31646200-31657400	Enhancers	Brain Anterior Caudate	brain
9	chr15:31646400-31655000	Enhancers	Fetal Heart	heart
10	chr15:31646400-31657400	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:31646600-31656800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr15:31646600-31657400	Weak transcription	HSMMtube	muscle
13	chr15:31646600-31657600	Weak transcription	HSMM	muscle
14	chr15:31646600-31658000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:31647600-31655600	Enhancers	Pancreas	Pancrea
16	chr15:31647600-31660800	Enhancers	Lung	lung
17	chr15:31648000-31660200	Enhancers	Stomach Mucosa	stomach
18	chr15:31649600-31654400	Enhancers	Esophagus	oesophagus
19	chr15:31649800-31655600	Enhancers	Small Intestine	intestine
20	chr15:31650200-31654600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:31650200-31657600	Weak transcription	Osteobl	bone
22	chr15:31650400-31655600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:31650600-31655200	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr15:31650600-31656200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:31651000-31654400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr15:31651200-31655200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr15:31651200-31660600	Enhancers	Fetal Intestine Large	intestine
28	chr15:31651400-31655400	Enhancers	Gastric	stomach
29	chr15:31651400-31657000	Enhancers	Brain Substantia Nigra	brain
30	chr15:31651400-31657400	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr15:31651600-31654400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr15:31651600-31654600	Enhancers	Fetal Brain Male	brain
33	chr15:31651600-31655200	Enhancers	Colon Smooth Muscle	Colon
34	chr15:31651800-31654600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:31651800-31654800	Enhancers	Fetal Brain Female	brain
36	chr15:31651800-31654800	Enhancers	Fetal Muscle Leg	muscle
37	chr15:31651800-31655400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:31651800-31655600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr15:31651800-31655600	Enhancers	Brain Angular Gyrus	brain
40	chr15:31652000-31654400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:31652000-31655000	Enhancers	Placenta	Placenta
42	chr15:31652000-31658400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:31652200-31654600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr15:31652200-31654600	Enhancers	Fetal Muscle Trunk	muscle
45	chr15:31652200-31654600	Flanking Active TSS	Dnd41	blood
46	chr15:31652200-31658400	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr15:31652200-31660000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:31652400-31654400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr15:31652400-31655200	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr15:31652400-31655600	Enhancers	Spleen	Spleen

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