Variant report

Variant	rs6456678
Chromosome Location	chr6:25359903-25359904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1013045	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1028347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1209305	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12173289	0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs12210416	0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs13211247	0.81[ASN][1000 genomes]
rs13217807	0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap]
rs1556043	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs169978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs177333	0.83[ASN][1000 genomes]
rs215009	0.87[ASN][1000 genomes]
rs215013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs215014	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2254974	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];0.86[AFR][1000 genomes]
rs2690059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690094	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2744234	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744237	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35361710	0.83[ASN][1000 genomes]
rs4712921	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4712922	0.88[ASN][1000 genomes]
rs6913927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6933921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760864	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7760906	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.98[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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6456678	HIST1H4A	cis	parietal	SCAN
rs6456678	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25352200-25363000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr6:25358200-25361000	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr6:25358800-25361400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:25358800-25362600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:25359000-25360000	Enhancers	Fetal Kidney	kidney
6	chr6:25359000-25360400	Enhancers	Brain Germinal Matrix	brain
7	chr6:25359000-25360800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:25359200-25360000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:25359200-25360000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr6:25359200-25360000	Enhancers	Lung	lung
11	chr6:25359200-25360400	Enhancers	Stomach Mucosa	stomach
12	chr6:25359200-25360600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:25359200-25360600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr6:25359200-25360800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:25359200-25361000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:25359200-25361000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:25359200-25361000	Enhancers	Ovary	ovary
18	chr6:25359200-25361000	Enhancers	Small Intestine	intestine
19	chr6:25359200-25361000	Enhancers	A549	lung
20	chr6:25359200-25361200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr6:25359200-25361200	Enhancers	Duodenum Mucosa	Duodenum
22	chr6:25359200-25361200	Enhancers	HSMM	muscle
23	chr6:25359200-25361400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:25359200-25362800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:25359200-25363600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:25359400-25360000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:25359400-25360000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:25359400-25360000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:25359400-25360000	Enhancers	Fetal Intestine Large	intestine
30	chr6:25359400-25360000	Enhancers	Right Atrium	heart
31	chr6:25359400-25360000	Flanking Active TSS	NH-A	brain
32	chr6:25359400-25360000	Flanking Active TSS	NHLF	lung
33	chr6:25359400-25360200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr6:25359400-25360200	Flanking Active TSS	Fetal Lung	lung
35	chr6:25359400-25360200	Flanking Active TSS	HMEC	breast
36	chr6:25359400-25360400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:25359400-25360400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:25359400-25360400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:25359400-25360400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:25359400-25360400	Enhancers	Placenta	Placenta
41	chr6:25359400-25360400	Enhancers	Gastric	stomach
42	chr6:25359400-25360400	Enhancers	Pancreas	Pancrea
43	chr6:25359400-25360400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:25359400-25360400	Flanking Active TSS	HSMMtube	muscle
45	chr6:25359400-25360400	Flanking Active TSS	Osteobl	bone
46	chr6:25359400-25361000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr6:25359400-25361000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:25359400-25361000	Enhancers	Fetal Intestine Small	intestine
49	chr6:25359400-25361000	Enhancers	Fetal Muscle Leg	muscle
50	chr6:25359400-25361000	Enhancers	Fetal Thymus	thymus

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