Variant report

Variant	rs2570219
Chromosome Location	chr15:52198001-52198002
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	NFIC	chr15:52197915-52198532	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr15:52197925-52198539	HCT-116	colon:	n/a	chr15:52198220-52198241 chr15:52198225-52198243
3	RAD21	chr15:52197925-52198511	HCT-116	colon:	n/a	chr15:52198223-52198242
4	NFIC	chr15:52197887-52198563	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr15:52197918-52198531	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52181216..52183971-chr15:52196238..52198437,3	MCF-7	breast:
2	chr15:52190968..52195310-chr15:52196264..52198737,5	MCF-7	breast:
3	chr15:52180707..52181542-chr15:52197867..52198459,2	MCF-7	breast:
4	chr15:52121176..52123509-chr15:52196902..52200014,3	MCF-7	breast:
5	chr15:52192386..52195436-chr15:52196990..52200236,4	MCF-7	breast:
6	chr15:52074254..52075293-chr15:52197801..52198638,3	MCF-7	breast:
7	chr15:52184376..52187037-chr15:52195725..52198410,2	K562	blood:

Variant related genes	Relation type
ENSG00000259201	TF binding region
ENSG00000272337	TF binding region
ENSG00000259201	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000128872	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1025185	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519323	1.00[EUR][1000 genomes]
rs10519325	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519326	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438469	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442283	1.00[EUR][1000 genomes]
rs1378891	1.00[EUR][1000 genomes]
rs1426085	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426086	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649047	1.00[EUR][1000 genomes]
rs17649178	1.00[EUR][1000 genomes]
rs17649255	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649391	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649692	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17649801	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17705530	1.00[EUR][1000 genomes]
rs17705649	1.00[EUR][1000 genomes]
rs17705685	1.00[EUR][1000 genomes]
rs17705889	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706076	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052707	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2162224	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263946	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2436664	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470609	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2470613	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554309	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554310	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554311	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554317	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554318	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554321	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554323	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554325	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554326	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554330	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554333	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554341	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2554351	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554352	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554356	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570218	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570220	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570221	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570225	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570227	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570232	0.85[AMR][1000 genomes]
rs2570234	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2570242	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570244	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570245	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570246	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570247	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570249	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570250	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570256	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570257	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570259	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570261	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570262	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570267	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570270	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570273	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2570274	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593165	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593175	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593176	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593180	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623246	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623248	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623250	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623252	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623253	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2623256	0.83[AMR][1000 genomes]
rs2623257	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623260	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623261	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2623264	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623267	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623268	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623269	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623277	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623278	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623287	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623293	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2899483	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2916174	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959297	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2959303	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099570	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34407523	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794533	1.00[EUR][1000 genomes]
rs3794537	1.00[EUR][1000 genomes]
rs4774600	1.00[EUR][1000 genomes]
rs4774601	1.00[EUR][1000 genomes]
rs4775979	1.00[EUR][1000 genomes]
rs4775987	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775988	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775989	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166322	1.00[EUR][1000 genomes]
rs7170429	1.00[EUR][1000 genomes]
rs7170700	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7173661	1.00[EUR][1000 genomes]
rs7179139	1.00[EUR][1000 genomes]
rs73411105	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013606	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8024441	1.00[EUR][1000 genomes]
rs8026507	1.00[EUR][1000 genomes]
rs8027426	1.00[EUR][1000 genomes]
rs8042310	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919056	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs919057	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990666	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 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	chr15:52156000-52211000	Weak transcription	Brain Substantia Nigra	brain
2	chr15:52167200-52210800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:52167600-52199600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:52171000-52210800	Weak transcription	Right Ventricle	heart
5	chr15:52172800-52208200	Weak transcription	Brain Angular Gyrus	brain
6	chr15:52177200-52213600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:52178800-52216600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:52179600-52203800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:52179800-52201600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:52179800-52218600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:52180200-52199400	Strong transcription	NHEK	skin
13	chr15:52180400-52218200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr15:52181200-52221000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr15:52181600-52203400	Strong transcription	Dnd41	blood
16	chr15:52181800-52203400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:52182800-52198600	Strong transcription	HMEC	breast
18	chr15:52183000-52203400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:52183200-52223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:52183400-52203200	Strong transcription	Primary T cells from cord blood	blood
21	chr15:52183600-52199000	Strong transcription	Fetal Intestine Large	intestine
22	chr15:52183800-52198200	Strong transcription	Liver	Liver
23	chr15:52184400-52205000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr15:52185600-52200000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:52185800-52204200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:52186200-52204200	Strong transcription	Primary B cells from cord blood	blood
27	chr15:52186400-52199400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:52186400-52200200	Strong transcription	Fetal Thymus	thymus
29	chr15:52186400-52204200	Strong transcription	Placenta	Placenta
30	chr15:52186400-52219000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:52187800-52212000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:52188200-52198200	Strong transcription	Hela-S3	cervix
33	chr15:52188200-52198600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr15:52188600-52200800	Strong transcription	K562	blood
35	chr15:52188600-52202400	Strong transcription	Adipose Nuclei	Adipose
36	chr15:52188600-52203600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr15:52191000-52198200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr15:52191000-52222800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:52191600-52199800	Weak transcription	Aorta	Aorta
40	chr15:52192800-52199600	Weak transcription	Lung	lung
41	chr15:52192800-52199800	Weak transcription	Gastric	stomach
42	chr15:52192800-52199800	Weak transcription	Pancreas	Pancrea
43	chr15:52192800-52213600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:52193400-52208200	Weak transcription	Esophagus	oesophagus
45	chr15:52193400-52209800	Weak transcription	HSMMtube	muscle
46	chr15:52193400-52210800	Weak transcription	Brain Germinal Matrix	brain
47	chr15:52193400-52227800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:52193400-52232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:52193600-52233600	Weak transcription	Fetal Brain Male	brain
50	chr15:52193800-52210400	Weak transcription	Brain Inferior Temporal Lobe	brain

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