Variant report

Variant	rs8038895
Chromosome Location	chr15:52069835-52069836
allele	C/T
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	CTCF	chr15:52068067-52069954	SK-N-SH	brain:	n/a	chr15:52069377-52069393 chr15:52069371-52069392 chr15:52069378-52069391 chr15:52069376-52069394 chr15:52068558-52068576 chr15:52068560-52068573 chr15:52068561-52068571
2	RAD21	chr15:52067986-52069923	SK-N-SH	brain:	n/a	chr15:52068560-52068570 chr15:52068559-52068572 chr15:52069374-52069393
3	ZKSCAN1	chr15:52069249-52069881	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr15:52069700-52069850	GM12875	blood:	n/a	n/a
5	CTCF	chr15:52067945-52069910	A549	lung:	n/a	chr15:52069377-52069393 chr15:52069371-52069392 chr15:52069378-52069391 chr15:52069376-52069394 chr15:52068558-52068576 chr15:52068560-52068573 chr15:52068561-52068571

No.	Distal block	Cell Line	Cell type
1	chr15:51939928..51943794-chr15:52067782..52071460,6	MCF-7	breast:
2	chr15:51941637..51943668-chr15:52068078..52069917,57	MCF-7	breast:
3	chr15:51942035..51944458-chr15:52068253..52069914,2	K562	blood:
4	chr15:51914398..51916260-chr15:52068370..52070743,2	MCF-7	breast:
5	chr15:51915397..51918003-chr15:52069309..52070981,2	MCF-7	breast:
6	chr15:51942270..51945778-chr15:52064444..52070724,6	MCF-7	breast:
7	chr15:52028103..52031226-chr15:52067709..52070826,4	MCF-7	breast:
8	chr15:51938680..51944458-chr15:52065543..52071230,9	K562	blood:
9	chr15:51941765..51942808-chr15:52067729..52069864,21	K562	blood:
10	chr15:52068519..52070724-chr15:52072830..52074753,2	K562	blood:

Variant related genes	Relation type
TMOD2	TF binding region
ENSG00000104093	Chromatin interaction
ENSG00000128872	Chromatin interaction
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16964486	1.00[YRI][hapmap]
rs17705373	1.00[YRI][hapmap]
rs17705685	1.00[YRI][hapmap]
rs3751595	1.00[YRI][hapmap]
rs3794533	1.00[YRI][hapmap]
rs7164550	1.00[AMR][1000 genomes]
rs7165594	1.00[YRI][hapmap]
rs7167759	1.00[YRI][hapmap]
rs7168503	1.00[AMR][1000 genomes]
rs7168775	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7180099	0.95[AFR][1000 genomes]
rs8034090	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs8035223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8039052	1.00[AFR][1000 genomes];1.00[AMR][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	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
2	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
4	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
5	chr15:52052400-52073200	Weak transcription	NHDF-Ad	bronchial
6	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:52052600-52106600	Weak transcription	HSMM	muscle
8	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
9	chr15:52058800-52072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:52060400-52079200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:52060400-52085400	Weak transcription	Fetal Lung	lung
13	chr15:52060600-52073400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:52060600-52073600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:52060600-52087400	Weak transcription	Gastric	stomach
16	chr15:52060600-52088400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:52060600-52091000	Weak transcription	Right Ventricle	heart
18	chr15:52060800-52074600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:52060800-52101200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:52060800-52102600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:52060800-52105400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:52061000-52074400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:52061600-52073600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:52061600-52085400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:52061600-52112000	Weak transcription	NHLF	lung
26	chr15:52061800-52073600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:52061800-52076200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:52061800-52077200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:52061800-52098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:52063000-52073000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:52063000-52074600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:52064400-52090400	Weak transcription	Left Ventricle	heart
33	chr15:52064600-52078400	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:52065600-52090600	Weak transcription	Spleen	Spleen
35	chr15:52065800-52070000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:52065800-52091000	Weak transcription	Esophagus	oesophagus
37	chr15:52067000-52073600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr15:52067200-52073600	Weak transcription	Primary B cells from cord blood	blood
39	chr15:52067200-52090600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:52067400-52072800	Weak transcription	Fetal Thymus	thymus
41	chr15:52067400-52073200	Weak transcription	Aorta	Aorta
42	chr15:52067400-52073200	Weak transcription	Ovary	ovary
43	chr15:52067400-52074600	Weak transcription	Dnd41	blood
44	chr15:52067400-52078400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:52067400-52079800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:52067600-52072000	Weak transcription	Fetal Brain Female	brain
47	chr15:52067600-52072800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:52067600-52073600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:52067600-52090600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:52067800-52072000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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