Variant report

Variant	rs16964585
Chromosome Location	chr15:52163909-52163910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52162237..52164985-chr15:52179856..52181914,2	K562	blood:
2	chr15:52162823..52165125-chr15:52167197..52169305,2	K562	blood:
3	chr15:52163617..52167105-chr15:52168428..52170438,3	MCF-7	breast:
4	chr15:52158309..52160218-chr15:52163470..52165265,2	MCF-7	breast:
5	chr15:52163038..52165507-chr15:52190093..52191832,2	MCF-7	breast:
6	chr15:52157498..52159871-chr15:52162459..52164030,2	K562	blood:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs16953082	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs16964488	1.00[CEU][hapmap]
rs16964505	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs16964506	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs16964507	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16964508	1.00[CEU][hapmap];0.82[JPT][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[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964555	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964561	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964579	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964596	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]
rs2570232	1.00[CEU][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]
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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52141600-52166800	Weak transcription	Stomach Mucosa	stomach
2	chr15:52141800-52176200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:52145800-52176600	Weak transcription	Psoas Muscle	Psoas
4	chr15:52148200-52176200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:52149400-52171000	Weak transcription	Brain Angular Gyrus	brain
6	chr15:52149800-52168000	Weak transcription	Right Ventricle	heart
7	chr15:52152400-52170000	Weak transcription	Pancreas	Pancrea
8	chr15:52152400-52170800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:52153800-52178000	Weak transcription	Brain Germinal Matrix	brain
10	chr15:52154400-52165800	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:52154400-52170200	Weak transcription	Fetal Brain Male	brain
12	chr15:52155000-52164000	Strong transcription	Primary B cells from cord blood	blood
13	chr15:52155000-52165400	Strong transcription	Dnd41	blood
14	chr15:52155000-52167600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:52155000-52167800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr15:52155000-52169800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr15:52155000-52170800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:52155000-52173600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr15:52155200-52167800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr15:52155200-52169600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:52155200-52170600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:52155400-52165400	Strong transcription	Thymus	Thymus
23	chr15:52155600-52164800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:52155600-52166400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr15:52155600-52192000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:52156000-52211000	Weak transcription	Brain Substantia Nigra	brain
27	chr15:52156400-52170600	Weak transcription	Brain Anterior Caudate	brain
28	chr15:52156800-52170000	Weak transcription	Spleen	Spleen
29	chr15:52157000-52166800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:52157000-52168600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:52157000-52170200	Weak transcription	Gastric	stomach
32	chr15:52157000-52170400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:52157000-52170800	Weak transcription	Fetal Kidney	kidney
34	chr15:52157200-52167000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:52157400-52166800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:52157600-52167400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:52157800-52164400	Weak transcription	Esophagus	oesophagus
38	chr15:52157800-52166800	Weak transcription	Colonic Mucosa	Colon
39	chr15:52157800-52178000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:52158000-52164400	Weak transcription	Lung	lung
41	chr15:52158000-52165200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:52158000-52167000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:52158000-52170800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:52158200-52168200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:52159000-52168600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:52159200-52165600	Strong transcription	Fetal Thymus	thymus
47	chr15:52159200-52166800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr15:52159400-52165600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:52159400-52165800	Strong transcription	Fetal Lung	lung
50	chr15:52159400-52166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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