Variant report

Variant	rs12904173
Chromosome Location	chr15:51829995-51829996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51828988..51832305-chr15:51839364..51844181,4	K562	blood:
2	chr15:51829420..51832370-chr15:51850921..51852494,2	K562	blood:
3	chr15:51828912..51831495-chr15:51835540..51837204,2	K562	blood:
4	chr15:51827562..51833709-chr15:51913512..51915889,5	MCF-7	breast:
5	chr15:51824663..51827027-chr15:51829318..51831016,2	K562	blood:
6	chr15:51828885..51831420-chr15:51912654..51914673,2	K562	blood:
7	chr15:51828366..51830744-chr15:51830911..51832606,2	MCF-7	breast:
8	chr15:51827966..51831646-chr15:51914070..51917015,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1017679	0.85[CEU][hapmap]
rs10851501	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070861	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11857716	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12324531	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441057	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12708427	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12901452	0.90[CEU][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs12904583	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1378892	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1378893	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1378894	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1378895	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1456295	0.90[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1456297	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1471072	0.85[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1551657	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17524750	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17524906	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1840707	0.90[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1902595	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1902596	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061425	0.95[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252220	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414112	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2445754	0.81[AFR][1000 genomes]
rs2446407	0.90[CEU][hapmap]
rs2459397	1.00[JPT][hapmap]
rs2459399	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs2470193	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs2606134	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2606136	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2606137	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs2606138	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2606139	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2606141	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2606143	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606145	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2606146	0.90[CEU][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2607110	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2607112	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2607116	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2607117	0.86[MEX][hapmap];0.91[TSI][hapmap]
rs2622768	0.83[EUR][1000 genomes]
rs2622769	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2622770	0.90[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs28408214	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34448759	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34532503	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34662965	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34929849	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35011964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35561856	0.83[EUR][1000 genomes]
rs3751585	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4465557	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4774594	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4775954	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55725532	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56879579	0.88[EUR][1000 genomes]
rs61618680	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493507	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493511	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6493512	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6493514	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs716986	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7180329	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7181921	0.87[MEX][hapmap];0.85[TSI][hapmap]
rs8025974	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs8026587	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs8027162	0.83[EUR][1000 genomes]
rs8029731	0.83[EUR][1000 genomes]
rs897581	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs956171	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9672605	0.83[EUR][1000 genomes]
rs9806214	0.81[EUR][1000 genomes]
rs9944266	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv904218	chr15:51743186-51873407	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv569405	chr15:51791559-51890282	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12904173	SCG3	cis	parietal	SCAN
rs12904173	SCG3	cis	cerebellum	SCAN
rs12904173	ATP8B4	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51776800-51837600	Weak transcription	Fetal Thymus	thymus
2	chr15:51776800-51855200	Weak transcription	Thymus	Thymus
3	chr15:51780400-51855800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:51780800-51839000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:51781400-51863000	Weak transcription	HSMM	muscle
6	chr15:51781600-51837000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:51787400-51855400	Weak transcription	Osteobl	bone
8	chr15:51792400-51838400	Weak transcription	HSMMtube	muscle
9	chr15:51794600-51861000	Weak transcription	Gastric	stomach
10	chr15:51809000-51854800	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:51816000-51861000	Weak transcription	Pancreas	Pancrea
12	chr15:51817000-51837800	Weak transcription	Brain Substantia Nigra	brain
13	chr15:51817200-51836400	Weak transcription	Aorta	Aorta
14	chr15:51817800-51862200	Weak transcription	Fetal Brain Male	brain
15	chr15:51818200-51847600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:51818200-51855400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:51818200-51861600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:51818400-51853400	Weak transcription	Lung	lung
19	chr15:51818400-51861200	Weak transcription	Fetal Stomach	stomach
20	chr15:51818800-51840200	Weak transcription	Hela-S3	cervix
21	chr15:51819200-51831400	Weak transcription	Fetal Heart	heart
22	chr15:51819200-51838200	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:51819400-51837600	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:51819400-51852600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:51819400-51853400	Weak transcription	Ovary	ovary
26	chr15:51819600-51853400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:51819600-51861400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:51819800-51830800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:51819800-51863000	Weak transcription	Right Ventricle	heart
30	chr15:51820000-51830400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:51822000-51849400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:51822400-51840000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr15:51822800-51830400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr15:51823000-51830200	Weak transcription	Primary T cells from cord blood	blood
35	chr15:51823600-51830600	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:51823600-51837000	Weak transcription	HMEC	breast
37	chr15:51824200-51837000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:51824400-51830800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:51824400-51854200	Weak transcription	Fetal Kidney	kidney
40	chr15:51824600-51830800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:51824600-51855000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:51824600-51860600	Weak transcription	Brain Anterior Caudate	brain
43	chr15:51824600-51861000	Weak transcription	Left Ventricle	heart
44	chr15:51824800-51836200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:51824800-51863200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:51825000-51831800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:51825000-51845600	Weak transcription	Brain Germinal Matrix	brain
48	chr15:51825600-51840000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:51826000-51853400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:51827000-51861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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