Variant report

Variant	rs129129
Chromosome Location	chr6:25961029-25961030
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	CBX3	chr6:25960833-25961290	K562	blood:	n/a	n/a
2	MAX	chr6:25960895-25961253	K562	blood:	n/a	n/a
3	SETDB1	chr6:25960779-25961471	U2OS	brain:	n/a	n/a
4	KAP1	chr6:25960724-25961299	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25959676..25961946-chr6:25964772..25967357,2	K562	blood:

Variant related genes	Relation type
TRIM38	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10425	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs115810	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1165176	0.81[CHD][hapmap]
rs1165201	0.96[CHD][hapmap];0.86[JPT][hapmap]
rs1165205	0.81[CHD][hapmap]
rs1165207	0.81[CHD][hapmap]
rs1185569	0.81[CHD][hapmap]
rs12346	0.87[CHD][hapmap]
rs1540275	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs1540276	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs169219	0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap]
rs175319	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189911	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs198810	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs198815	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs198820	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs198845	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs198848	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs198852	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs198853	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs199725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199727	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs199734	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199736	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199737	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199739	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199741	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs199743	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs199748	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs199750	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs199751	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs199752	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap]
rs199753	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs199754	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs199755	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2032447	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2051540	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213284	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs2230655	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs428469	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4401650	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs442601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478349	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs531750	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs537581	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs599444	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs629835	0.84[JPT][hapmap]
rs645279	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6901039	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6922788	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs7756117	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs7767546	0.84[ASN][1000 genomes]
rs807212	1.00[CHB][hapmap]
rs807214	1.00[CHB][hapmap]
rs9356995	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9379811	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467664	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs129129	HIST1H2BD	cis	multi-tissue	Pritchard
rs129129	HIST1H2AJ	cis	parietal	SCAN
rs129129	HIST1H4I	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25956000-25963000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25958400-25962200	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:25958600-25962000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:25958800-25961800	Enhancers	Primary B cells from cord blood	blood
5	chr6:25959000-25961800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:25959000-25962200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr6:25959200-25961600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:25959200-25961600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:25959200-25961800	Weak transcription	HUVEC	blood vessel
10	chr6:25959200-25962000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:25959400-25961400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:25959400-25961600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:25959400-25961800	Weak transcription	Spleen	Spleen
14	chr6:25959600-25961800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:25959600-25962200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:25959600-25962400	Enhancers	Fetal Muscle Leg	muscle
17	chr6:25959800-25961200	Enhancers	NHDF-Ad	bronchial
18	chr6:25959800-25961600	Weak transcription	Primary T cells from cord blood	blood
19	chr6:25959800-25962000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:25959800-25962000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25959800-25962200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr6:25959800-25962200	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:25959800-25962200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:25960000-25961600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:25960000-25961600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr6:25960000-25961800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:25960000-25961800	Weak transcription	Right Atrium	heart
28	chr6:25960400-25961200	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr6:25960400-25962000	Weak transcription	Thymus	Thymus
30	chr6:25960400-25962000	Weak transcription	HMEC	breast
31	chr6:25960600-25961600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:25960600-25961800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:25960600-25961800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr6:25960600-25961800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:25960600-25962000	Weak transcription	NHEK	skin
36	chr6:25960600-25962200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:25960600-25962400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:25960800-25961800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:25960800-25961800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr6:25960800-25962000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:25960800-25962000	Enhancers	HSMM	muscle
42	chr6:25960800-25962200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:25960800-25962200	Enhancers	GM12878-XiMat	blood
44	chr6:25960800-25962400	Weak transcription	Psoas Muscle	Psoas
45	chr6:25961000-25961200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:25961000-25961200	Flanking Active TSS	HSMMtube	muscle
47	chr6:25961000-25961400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:25961000-25962000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:25961000-25962200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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