Variant report

Variant	rs6933921
Chromosome Location	chr6:25364017-25364018
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	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1028347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1209305	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[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];0.87[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];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs215014	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2254974	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2690059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690094	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2744234	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[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];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35361710	0.83[ASN][1000 genomes]
rs4712921	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4712922	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6456678	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]
rs6913927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs760864	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7760906	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.86[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
rs6933921	HIST1H4A	cis	parietal	SCAN
rs6933921	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25359600-25366000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr6:25359800-25367200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:25360000-25367200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:25360000-25367400	Weak transcription	Lung	lung
5	chr6:25360000-25367400	Weak transcription	Right Atrium	heart
6	chr6:25360400-25366000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr6:25360400-25366400	Weak transcription	Gastric	stomach
8	chr6:25360400-25367600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:25360400-25367600	Weak transcription	Pancreas	Pancrea
10	chr6:25360400-25367800	Weak transcription	Brain Germinal Matrix	brain
11	chr6:25360400-25369200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:25360600-25365600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:25360800-25367200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:25360800-25367600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:25360800-25369800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:25361000-25364200	Weak transcription	Fetal Thymus	thymus
17	chr6:25361000-25365000	Weak transcription	Ovary	ovary
18	chr6:25361000-25365600	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:25361000-25367000	Weak transcription	Fetal Intestine Small	intestine
20	chr6:25361000-25367200	Weak transcription	Fetal Intestine Large	intestine
21	chr6:25361000-25367200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:25361000-25367400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:25361000-25369200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:25361000-25369400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:25361000-25369400	Weak transcription	Left Ventricle	heart
26	chr6:25361000-25369800	Weak transcription	Brain Substantia Nigra	brain
27	chr6:25361200-25366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:25361200-25366600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:25361200-25367200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:25361400-25365400	Weak transcription	Thymus	Thymus
31	chr6:25362000-25367000	Weak transcription	NHLF	lung
32	chr6:25362000-25367200	Weak transcription	Brain Anterior Caudate	brain
33	chr6:25362600-25367200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:25362800-25366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:25362800-25367600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:25363000-25366000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr6:25363000-25366400	Weak transcription	NHEK	skin
38	chr6:25363200-25364200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:25363200-25364400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:25363200-25364400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:25363200-25364600	Enhancers	Primary hematopoietic stem cells	blood
42	chr6:25363200-25365400	Weak transcription	Aorta	Aorta
43	chr6:25363200-25365800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr6:25363400-25364400	Enhancers	Adipose Nuclei	Adipose
45	chr6:25363400-25367200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:25363600-25364200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:25363600-25366200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:25363800-25364200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:25363800-25366200	Weak transcription	HMEC	breast
50	chr6:25363800-25366600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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