Variant report

Variant	rs12898535
Chromosome Location	chr15:78359415-78359416
allele	A/C
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	GATA3	chr15:78359413-78361164	SK-N-SH	brain:	n/a	chr15:78360539-78360546
2	TCF12	chr15:78359394-78361102	SK-N-SH	brain:	n/a	chr15:78361078-78361087
3	EP300	chr15:78358540-78361397	SK-N-SH	brain:	n/a	chr15:78360191-78360205 chr15:78361188-78361198 chr15:78360535-78360543
4	USF2	chr15:78359178-78360442	Hela-S3	cervix:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D2B-4	chr15:78357257-78359670	l_1195_chr15:78344341-78421177_testes

Variant related genes	Relation type
TBC1D2B	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1053506	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10775214	1.00[YRI][hapmap]
rs10775215	1.00[ASN][1000 genomes]
rs11072725	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072726	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11633329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633569	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636889	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854102	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12595595	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900731	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901492	1.00[ASN][1000 genomes]
rs12913206	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12915731	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12915847	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916320	1.00[ASN][1000 genomes]
rs1348256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969502	1.00[CEU][hapmap]
rs17477813	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs1837911	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1837912	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015951	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044100	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680277	1.00[ASN][1000 genomes]
rs3972617	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243072	1.00[ASN][1000 genomes]
rs4243073	0.86[AFR][1000 genomes]
rs4316722	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4411474	1.00[ASN][1000 genomes]
rs4886551	1.00[ASN][1000 genomes]
rs4886552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886985	1.00[ASN][1000 genomes]
rs4886986	1.00[ASN][1000 genomes]
rs4886987	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886990	1.00[ASN][1000 genomes]
rs4886991	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886993	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886997	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886998	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887001	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887003	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4887004	1.00[ASN][1000 genomes]
rs4997420	0.84[AFR][1000 genomes]
rs61732053	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163997	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7169381	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7169882	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170101	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170286	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170452	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174640	1.00[CEU][hapmap]
rs7175192	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175235	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175975	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180684	1.00[JPT][hapmap]
rs8025423	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033216	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894295	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894296	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894302	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788640	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920180	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78344800-78359800	Weak transcription	Fetal Brain Female	brain
2	chr15:78347400-78367800	Enhancers	Placenta	Placenta
3	chr15:78349400-78360800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:78354200-78359600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr15:78354200-78360600	Enhancers	Colon Smooth Muscle	Colon
6	chr15:78354200-78363200	Enhancers	Fetal Intestine Large	intestine
7	chr15:78354200-78363200	Enhancers	Stomach Mucosa	stomach
8	chr15:78354200-78366400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:78354600-78365400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr15:78354600-78366400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr15:78354800-78359600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr15:78354800-78359800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:78354800-78360800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:78354800-78360800	Enhancers	Brain Anterior Caudate	brain
15	chr15:78354800-78362600	Enhancers	Fetal Kidney	kidney
16	chr15:78354800-78362800	Enhancers	HSMMtube	muscle
17	chr15:78355000-78360800	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr15:78355000-78363200	Enhancers	Brain Substantia Nigra	brain
19	chr15:78355200-78360800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:78355200-78362800	Enhancers	Pancreas	Pancrea
21	chr15:78355200-78364000	Enhancers	Dnd41	blood
22	chr15:78355400-78359800	Weak transcription	Brain Germinal Matrix	brain
23	chr15:78355600-78365400	Enhancers	Small Intestine	intestine
24	chr15:78355800-78360800	Enhancers	Rectal Smooth Muscle	rectum
25	chr15:78355800-78363000	Enhancers	Spleen	Spleen
26	chr15:78355800-78363200	Enhancers	Right Atrium	heart
27	chr15:78355800-78364000	Enhancers	Fetal Muscle Leg	muscle
28	chr15:78356000-78363000	Enhancers	Brain Angular Gyrus	brain
29	chr15:78356000-78363800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:78356200-78362800	Enhancers	Psoas Muscle	Psoas
31	chr15:78356200-78363000	Enhancers	Fetal Stomach	stomach
32	chr15:78356400-78361000	Enhancers	HUVEC	blood vessel
33	chr15:78356400-78363000	Enhancers	Brain Cingulate Gyrus	brain
34	chr15:78356600-78359600	Weak transcription	Ovary	ovary
35	chr15:78356600-78360800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr15:78356600-78362400	Enhancers	Fetal Lung	lung
37	chr15:78356800-78359800	Weak transcription	Fetal Brain Male	brain
38	chr15:78357000-78361000	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:78357000-78363200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr15:78357200-78360800	Enhancers	Primary B cells from cord blood	blood
41	chr15:78357200-78363000	Enhancers	Primary B cells from peripheral blood	blood
42	chr15:78357400-78359800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr15:78357400-78361200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:78357400-78361200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:78357400-78361800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:78357400-78364400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:78357400-78365000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr15:78357600-78360200	Genic enhancers	Fetal Intestine Small	intestine
49	chr15:78357600-78360600	Enhancers	Colonic Mucosa	Colon
50	chr15:78357600-78362800	Enhancers	H1 Cell Line	embryonic stem cell

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