Variant report

Variant	rs16964596
Chromosome Location	chr15:52176644-52176645
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	chr15:52176545-52177146	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52175882..52177402-chr15:52311052..52312787,2	K562	blood:
2	chr15:52121304..52123293-chr15:52174334..52178063,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207484	TF binding region
ENSG00000138594	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs16953082	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964486	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs16964488	1.00[CEU][hapmap]
rs16964505	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.90[EUR][1000 genomes]
rs16964506	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs16964507	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap];0.90[EUR][1000 genomes]
rs16964508	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs16964510	0.90[EUR][1000 genomes]
rs16964518	0.90[EUR][1000 genomes]
rs16964528	0.88[EUR][1000 genomes]
rs16964532	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964555	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964579	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964585	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964639	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964645	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17705373	1.00[CEU][hapmap]
rs1991267	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2258248	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2414115	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2570232	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes]
rs2570265	0.90[ASN][1000 genomes]
rs2593181	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2593184	0.90[ASN][1000 genomes]
rs2623256	0.84[EUR][1000 genomes]
rs2623291	0.90[ASN][1000 genomes]
rs2899478	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2959296	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3751595	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs3794529	0.83[EUR][1000 genomes]
rs4775971	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4775988	1.00[YRI][hapmap]
rs56221158	0.88[EUR][1000 genomes]
rs7165594	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7167759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7174616	1.00[CEU][hapmap]
rs7175121	1.00[CEU][hapmap]
rs7342575	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs74015757	0.81[EUR][1000 genomes]
rs74015761	0.81[EUR][1000 genomes]
rs8036648	0.85[EUR][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:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52153800-52178000	Weak transcription	Brain Germinal Matrix	brain
2	chr15:52155600-52192000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:52156000-52211000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:52157800-52178000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:52163000-52186800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:52163200-52184200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:52163400-52181400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr15:52163400-52186200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:52165200-52181800	Weak transcription	Esophagus	oesophagus
10	chr15:52165800-52183600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:52167200-52186200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:52167200-52210800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:52167600-52177000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:52167600-52177000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:52167600-52192000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:52167600-52199600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:52167800-52176800	Weak transcription	Dnd41	blood
18	chr15:52167800-52181400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:52167800-52188600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:52168200-52183200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:52168600-52188600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:52168800-52183800	Weak transcription	Fetal Thymus	thymus
23	chr15:52169200-52179600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:52169400-52179800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:52169800-52181200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr15:52170400-52178000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:52170400-52179800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr15:52170400-52186400	Weak transcription	Thymus	Thymus
29	chr15:52170400-52186600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:52170600-52176800	Weak transcription	GM12878-XiMat	blood
31	chr15:52170600-52178200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:52170600-52181800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:52170600-52184800	Weak transcription	Lung	lung
34	chr15:52170600-52186000	Weak transcription	Left Ventricle	heart
35	chr15:52171000-52180200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:52171000-52180400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:52171000-52184400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:52171000-52210800	Weak transcription	Right Ventricle	heart
39	chr15:52171200-52179800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:52171200-52190200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:52171400-52180200	Weak transcription	Liver	Liver
42	chr15:52171400-52181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:52171600-52179600	Weak transcription	HepG2	liver
44	chr15:52171600-52187000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:52171800-52183000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:52172200-52178200	Weak transcription	Fetal Intestine Large	intestine
47	chr15:52172200-52181800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:52172200-52186000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr15:52172200-52186600	Weak transcription	Fetal Kidney	kidney
50	chr15:52172200-52190200	Weak transcription	Fetal Heart	heart

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