Variant report

Variant	rs12900731
Chromosome Location	chr15:78291045-78291046
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78290955..78292806-chr15:79043518..79045037,2	MCF-7	breast:
2	chr15:78290983..78293923-chr15:78293965..78296117,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CIB2-4	chr15:78290861-78291351	NONHSAT047525

Variant related genes	Relation type
ENSG00000238166	Chromatin interaction
ENSG00000167202	Chromatin interaction

Extended variants
information (count: 68 )
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];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10775214	0.87[ASW][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs10775215	1.00[ASN][1000 genomes]
rs11072725	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072726	0.87[ASW][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs11633329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633569	0.94[AFR][1000 genomes];0.98[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];0.91[AFR][1000 genomes];0.81[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];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898535	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];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12915847	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]
rs12916320	1.00[ASN][1000 genomes]
rs1348256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969502	1.00[CEU][hapmap]
rs17477813	0.93[ASW][hapmap];0.85[YRI][hapmap]
rs1837911	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1837912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[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];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044100	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2867984	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680277	1.00[ASN][1000 genomes]
rs3972617	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243072	1.00[ASN][1000 genomes]
rs4316722	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4377127	0.85[GIH][hapmap];0.92[TSI][hapmap]
rs4411474	1.00[ASN][1000 genomes]
rs4886551	1.00[ASN][1000 genomes]
rs4886552	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886556	0.92[AFR][1000 genomes];0.81[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];0.94[AFR][1000 genomes];0.98[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];0.91[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];0.91[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];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.81[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];0.91[AFR][1000 genomes];0.81[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];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887002	0.91[AFR][1000 genomes];0.81[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];0.81[AMR][1000 genomes]
rs61732053	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163997	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7169882	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170101	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];0.88[AFR][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];0.91[AFR][1000 genomes];0.81[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];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174640	1.00[CEU][hapmap]
rs7175192	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175235	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175975	0.91[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];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030999	0.82[ASW][hapmap]
rs8033216	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];0.91[AFR][1000 genomes];0.81[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];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894296	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.81[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];0.94[AFR][1000 genomes];0.98[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];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920180	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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	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
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78280200-78295800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:78283400-78291200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:78283400-78292800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:78283400-78293400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:78283400-78296400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:78283400-78305000	Weak transcription	K562	blood
7	chr15:78283600-78294800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:78283600-78300800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:78283800-78301000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:78284600-78310200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:78284800-78296400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:78285400-78295800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:78285400-78304400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:78285800-78299200	Strong transcription	Fetal Intestine Large	intestine
15	chr15:78285800-78309600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:78286000-78310400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr15:78286400-78292200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:78286400-78295200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:78286600-78293400	Weak transcription	Brain Germinal Matrix	brain
20	chr15:78286600-78293400	Weak transcription	Small Intestine	intestine
21	chr15:78286600-78296400	Strong transcription	Fetal Intestine Small	intestine
22	chr15:78286800-78295200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:78287000-78293400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:78287000-78316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:78287600-78293400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:78287600-78295400	Weak transcription	Psoas Muscle	Psoas
27	chr15:78287800-78297400	Weak transcription	A549	lung
28	chr15:78288000-78294800	Weak transcription	HUVEC	blood vessel
29	chr15:78288200-78293000	Weak transcription	NH-A	brain
30	chr15:78288400-78292400	Strong transcription	Liver	Liver
31	chr15:78288400-78311000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr15:78288600-78291400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr15:78288600-78292200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr15:78288600-78292400	Strong transcription	Lung	lung
35	chr15:78288600-78297000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:78288600-78303000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:78288600-78304400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:78288600-78309600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:78288600-78309600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:78288600-78309600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:78288600-78309600	Strong transcription	Thymus	Thymus
42	chr15:78288800-78292800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:78288800-78292800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr15:78288800-78292800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:78288800-78293200	Genic enhancers	Fetal Muscle Leg	muscle
46	chr15:78288800-78295200	Weak transcription	HMEC	breast
47	chr15:78288800-78304800	Weak transcription	Fetal Kidney	kidney
48	chr15:78288800-78309600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:78288800-78310400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr15:78289000-78292600	Strong transcription	Placenta	Placenta

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