Variant report

Variant	rs6864641
Chromosome Location	chr5:14750251-14750252
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	GATA3	chr5:14749886-14750387	SK-N-SH	brain:	n/a	n/a
2	EP300	chr5:14749919-14750382	SK-N-SH_RA	brain:	n/a	n/a
3	PBX3	chr5:14749968-14750466	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:14750060-14750260	K562	blood:	n/a	n/a
5	EP300	chr5:14749890-14750411	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ANKH	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10080009	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs13170282	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13182007	0.94[ASN][1000 genomes]
rs149391	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149554	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152363	0.81[CHB][hapmap]
rs152364	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153920	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153927	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153928	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153929	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153930	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153932	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153933	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1679140	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16903680	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs16903681	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs16903692	0.81[CHB][hapmap]
rs16903693	0.84[CHB][hapmap]
rs1697124	1.00[CEU][hapmap]
rs192218	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288474	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs31934	0.85[YRI][hapmap]
rs34106421	0.95[ASN][1000 genomes]
rs35628922	0.97[ASN][1000 genomes]
rs35971379	0.94[ASN][1000 genomes]
rs4702046	0.95[ASN][1000 genomes]
rs4702047	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4702048	0.91[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs6895129	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs696035	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs696294	0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs696295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697566	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs697567	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697568	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697571	0.92[GIH][hapmap]
rs7734375	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs875525	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs891051	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2756652	chr5:14745268-14750481	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14725400-14758600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:14727200-14757000	Weak transcription	NHLF	lung
3	chr5:14729200-14791000	Weak transcription	Small Intestine	intestine
4	chr5:14729600-14752600	Strong transcription	Fetal Intestine Large	intestine
5	chr5:14730000-14758400	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr5:14733400-14750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:14733400-14753000	Weak transcription	Fetal Brain Male	brain
8	chr5:14736600-14752200	Strong transcription	Stomach Smooth Muscle	stomach
9	chr5:14736600-14760000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:14736800-14752800	Weak transcription	A549	lung
11	chr5:14736800-14753800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr5:14736800-14757400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr5:14737000-14754200	Strong transcription	Liver	Liver
14	chr5:14737800-14759200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr5:14737800-14759400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:14739600-14753800	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:14739800-14751200	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:14740800-14751400	Strong transcription	Adipose Nuclei	Adipose
19	chr5:14740800-14755200	Weak transcription	NHDF-Ad	bronchial
20	chr5:14741000-14752000	Weak transcription	Fetal Lung	lung
21	chr5:14741600-14753800	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:14741600-14767800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:14741800-14750400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:14742000-14751600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
25	chr5:14742400-14752600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:14742800-14756600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:14742800-14758400	Strong transcription	Primary T cells from cord blood	blood
28	chr5:14743000-14756800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:14744200-14757400	Strong transcription	Dnd41	blood
30	chr5:14744600-14751000	Strong transcription	Fetal Brain Female	brain
31	chr5:14744600-14758600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:14744600-14761800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:14744600-14775800	Weak transcription	NH-A	brain
34	chr5:14744800-14751000	Strong transcription	Brain Germinal Matrix	brain
35	chr5:14744800-14751400	Strong transcription	Brain Anterior Caudate	brain
36	chr5:14744800-14757200	Weak transcription	HUVEC	blood vessel
37	chr5:14744800-14776000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:14745000-14754600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:14745000-14756200	Strong transcription	Osteobl	bone
40	chr5:14745200-14751600	Strong transcription	Brain Hippocampus Middle	brain
41	chr5:14745200-14751600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr5:14745200-14753600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr5:14745400-14751600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:14745400-14751600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr5:14745800-14751400	Strong transcription	Brain Angular Gyrus	brain
46	chr5:14745800-14757800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:14746000-14790200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr5:14746200-14751200	Strong transcription	Brain Substantia Nigra	brain
49	chr5:14746200-14751400	Strong transcription	Left Ventricle	heart
50	chr5:14746200-14760200	Weak transcription	Fetal Muscle Leg	muscle

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