Variant report

Variant	rs12904938
Chromosome Location	chr15:77721225-77721226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77715788..77717648-chr15:77719796..77722237,2	K562	blood:
2	chr15:77712031..77719483-chr15:77720000..77723368,8	K562	blood:
3	chr15:77709335..77715793-chr15:77716367..77723204,14	MCF-7	breast:
4	chr15:77720681..77722687-chr15:77725659..77728094,2	K562	blood:
5	chr15:77711837..77714801-chr15:77720000..77724224,8	K562	blood:
6	chr15:77673612..77675900-chr15:77720669..77722192,2	K562	blood:

Variant related genes	Relation type
ENSG00000140382	Chromatin interaction
ENSG00000173517	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1005752	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10152181	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1022172	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072653	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11632966	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11633054	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636554	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11852471	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11857294	0.83[ASN][1000 genomes]
rs11857450	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11858641	0.81[ASN][1000 genomes]
rs1191196	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12324627	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901503	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12905951	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12906708	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12910361	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12910480	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12911371	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12912050	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12914345	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1389436	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1473922	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1493700	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1565756	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565757	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1602925	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2055901	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2175941	0.81[ASN][1000 genomes]
rs28584877	0.80[ASN][1000 genomes]
rs34591043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886515	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4886858	0.94[ASN][1000 genomes]
rs4886862	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4886866	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4886869	0.92[ASN][1000 genomes]
rs59153558	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62007299	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62008452	0.81[ASN][1000 genomes]
rs6495240	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119	0.86[AFR][1000 genomes]
rs7166927	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7167794	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7170877	0.80[EUR][1000 genomes]
rs7175674	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7176302	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7178572	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8024485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030074	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8034133	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037561	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs952471	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952472	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs965480	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77714000-77726400	Weak transcription	Small Intestine	intestine
2	chr15:77714000-77727600	Weak transcription	Left Ventricle	heart
3	chr15:77714000-77748600	Weak transcription	Placenta	Placenta
4	chr15:77714200-77721400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr15:77714400-77722600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:77714400-77722800	Weak transcription	Right Ventricle	heart
7	chr15:77714400-77732400	Weak transcription	HSMM	muscle
8	chr15:77714400-77732800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:77714400-77739200	Weak transcription	Right Atrium	heart
10	chr15:77714400-77741600	Weak transcription	Fetal Thymus	thymus
11	chr15:77714600-77722400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:77714600-77722600	Weak transcription	Brain Angular Gyrus	brain
13	chr15:77714600-77727400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:77714600-77732800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:77714600-77734400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:77714800-77723800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr15:77714800-77739200	Weak transcription	Fetal Intestine Small	intestine
18	chr15:77715000-77740600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:77715400-77733800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:77715400-77737800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:77716000-77733800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:77716200-77730200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:77716400-77734200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:77716400-77741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:77716800-77738000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:77716800-77742600	Weak transcription	Hela-S3	cervix
27	chr15:77717000-77728400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:77717000-77732800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:77717000-77754400	Weak transcription	K562	blood
30	chr15:77717200-77739400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:77717800-77725400	Weak transcription	Psoas Muscle	Psoas
32	chr15:77717800-77726400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:77717800-77732600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:77718800-77732000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:77719600-77722000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:77719600-77722800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:77719800-77729000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:77720000-77739400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:77720200-77721600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:77720200-77743000	Weak transcription	Primary B cells from cord blood	blood
41	chr15:77720400-77722000	Weak transcription	GM12878-XiMat	blood
42	chr15:77720400-77722600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:77720400-77722800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:77720600-77722200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:77720600-77722600	Weak transcription	Primary T cells from cord blood	blood
46	chr15:77720600-77722600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr15:77720800-77729000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:77721200-77729000	Weak transcription	Primary B cells from peripheral blood	blood

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