Variant report

Variant	rs28534445
Chromosome Location	chr15:50641385-50641386
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	POLR2A	chr15:50641221-50643664	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50474061..50475974-chr15:50641012..50643370,2	MCF-7	breast:
2	chr15:50487139..50490001-chr15:50641333..50643043,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HDC-2	chr15:50641135-50647076	NONHSAT042404

Variant related genes	Relation type
ENSG00000271819	TF binding region
ENSG00000140284	Chromatin interaction
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11070766	0.91[ASN][1000 genomes]
rs11070768	0.91[ASN][1000 genomes]
rs11629603	0.95[ASN][1000 genomes]
rs11630045	0.88[ASN][1000 genomes]
rs11630063	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11631197	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11631985	0.95[ASN][1000 genomes]
rs11632019	0.91[ASN][1000 genomes]
rs11632703	0.91[ASN][1000 genomes]
rs11636564	0.91[ASN][1000 genomes]
rs11636908	0.95[ASN][1000 genomes]
rs11637901	0.95[ASN][1000 genomes]
rs11637975	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11638432	0.91[ASN][1000 genomes]
rs11638564	0.95[ASN][1000 genomes]
rs11639406	0.95[ASN][1000 genomes]
rs11852487	0.91[ASN][1000 genomes]
rs11853236	0.91[ASN][1000 genomes]
rs11855823	0.91[ASN][1000 genomes]
rs12902318	0.95[ASN][1000 genomes]
rs12904469	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12904711	0.94[EUR][1000 genomes]
rs12906304	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12908591	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909337	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910368	0.95[ASN][1000 genomes]
rs12910586	0.91[ASN][1000 genomes]
rs12912679	1.00[ASN][1000 genomes]
rs12912969	0.95[ASN][1000 genomes]
rs12923	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1645	0.95[ASN][1000 genomes]
rs16963604	0.91[ASN][1000 genomes]
rs16963612	0.91[ASN][1000 genomes]
rs17508371	0.88[ASN][1000 genomes]
rs1972700	0.87[ASN][1000 genomes]
rs2033115	0.95[ASN][1000 genomes]
rs2081628	0.95[ASN][1000 genomes]
rs28372114	0.91[ASN][1000 genomes]
rs28408662	0.95[ASN][1000 genomes]
rs28451583	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28453939	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28531946	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28609286	0.91[ASN][1000 genomes]
rs28669213	0.88[ASN][1000 genomes]
rs28688566	0.95[ASN][1000 genomes]
rs28690939	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715646	0.95[ASN][1000 genomes]
rs28716586	0.95[ASN][1000 genomes]
rs28719982	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34143694	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34197276	0.91[ASN][1000 genomes]
rs34312018	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34405772	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34590486	0.95[ASN][1000 genomes]
rs35000991	0.95[ASN][1000 genomes]
rs35013067	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35024305	0.91[ASN][1000 genomes]
rs35033384	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35168369	0.95[ASN][1000 genomes]
rs35354250	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35446819	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35453213	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774559	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775872	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4775873	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775874	0.91[ASN][1000 genomes]
rs4775875	0.91[ASN][1000 genomes]
rs4775876	0.91[ASN][1000 genomes]
rs4775877	0.95[ASN][1000 genomes]
rs526045	0.95[ASN][1000 genomes]
rs526952	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022571	0.84[ASN][1000 genomes]
rs6493429	0.86[ASN][1000 genomes]
rs7163457	0.95[ASN][1000 genomes]
rs7164375	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164377	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164798	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173127	0.88[ASN][1000 genomes]
rs7175150	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7176792	0.91[ASN][1000 genomes]
rs7183422	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73399285	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8024514	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025367	0.95[ASN][1000 genomes]
rs8026571	0.95[ASN][1000 genomes]
rs8027367	0.95[ASN][1000 genomes]
rs8030952	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034597	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8034615	0.95[ASN][1000 genomes]
rs8036354	0.88[ASN][1000 genomes]
rs8042053	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8043475	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50600800-50641400	Weak transcription	HSMM	muscle
2	chr15:50600800-50641600	Weak transcription	Fetal Kidney	kidney
3	chr15:50600800-50643000	Weak transcription	Fetal Thymus	thymus
4	chr15:50600800-50643400	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:50600800-50644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:50600800-50644600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:50601400-50642800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:50608800-50642800	Weak transcription	Hela-S3	cervix
9	chr15:50615200-50644000	Weak transcription	HSMMtube	muscle
10	chr15:50618200-50642400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:50618400-50646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:50620400-50641800	Weak transcription	Adipose Nuclei	Adipose
13	chr15:50621200-50646000	Weak transcription	Gastric	stomach
14	chr15:50622000-50642400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:50623400-50643000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:50623800-50644200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:50623800-50645600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:50624000-50644000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:50624000-50644000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:50624000-50644000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:50625600-50641600	Weak transcription	Osteobl	bone
22	chr15:50626000-50641400	Weak transcription	Dnd41	blood
23	chr15:50627400-50641400	Weak transcription	Fetal Brain Female	brain
24	chr15:50627600-50642400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:50627600-50643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:50627800-50641600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:50627800-50643600	Weak transcription	Lung	lung
28	chr15:50628200-50641400	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:50628400-50643600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr15:50629000-50642800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:50630000-50641600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:50630000-50641600	Weak transcription	GM12878-XiMat	blood
33	chr15:50630000-50643600	Weak transcription	Placenta	Placenta
34	chr15:50630400-50641600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:50631000-50641400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:50631000-50643400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:50631400-50643400	Weak transcription	Fetal Stomach	stomach
38	chr15:50631400-50643800	Weak transcription	Fetal Intestine Small	intestine
39	chr15:50631600-50642400	Weak transcription	Thymus	Thymus
40	chr15:50632800-50641600	Weak transcription	K562	blood
41	chr15:50633000-50641600	Weak transcription	NHLF	lung
42	chr15:50633600-50641400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:50633800-50645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:50634400-50642200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:50634400-50642200	Weak transcription	Small Intestine	intestine
46	chr15:50635800-50643600	Weak transcription	Psoas Muscle	Psoas
47	chr15:50636400-50642400	Weak transcription	Fetal Lung	lung
48	chr15:50636800-50642200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:50637000-50641600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:50637200-50641600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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