Variant report

Variant	rs909728
Chromosome Location	chr6:29719561-29719562
allele	A/G
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	ZC3H11A	chr6:29719372-29719641	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:29718134..29720156-chr6:31462731..31465532,2	MCF-7	breast:
2	chr6:29595494..29598412-chr6:29717928..29720060,2	K562	blood:
3	chr6:29719431..29722230-chr6:29728984..29731849,2	MCF-7	breast:

Variant related genes	Relation type
IFITM4P	TF binding region
HLA-F-AS1	TF binding region
MICE	TF binding region
ENSG00000201680	Chromatin interaction
ENSG00000204681	Chromatin interaction
ENSG00000270896	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1610622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610733	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610734	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610741	0.80[ASN][1000 genomes]
rs1623122	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1633080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633084	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633085	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633089	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16867712	0.88[ASN][1000 genomes]
rs1737083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737085	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2394164	0.85[ASN][1000 genomes]
rs34260811	0.89[ASN][1000 genomes]
rs4713237	0.83[ASN][1000 genomes]
rs4713239	0.88[ASN][1000 genomes]
rs4713240	0.90[ASN][1000 genomes]
rs4713242	0.85[ASN][1000 genomes]
rs4713244	0.89[ASN][1000 genomes]
rs760145	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7754067	0.85[ASN][1000 genomes]
rs7759474	0.86[ASN][1000 genomes]
rs7759482	0.81[ASN][1000 genomes]
rs909729	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368609	0.88[ASN][1000 genomes]
rs9391660	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv969373	chr6:29717694-29719688	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs909728	HIST1H2AH	cis	cerebellum	SCAN
rs909728	HLA-A	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29717000-29720000	Enhancers	Spleen	Spleen
2	chr6:29717200-29719600	Weak transcription	HSMM	muscle
3	chr6:29717400-29719600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:29717400-29719600	Weak transcription	A549	lung
5	chr6:29717400-29719600	Weak transcription	HUVEC	blood vessel
6	chr6:29717400-29719800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:29717400-29719800	Enhancers	Left Ventricle	heart
8	chr6:29717400-29719800	Weak transcription	HSMMtube	muscle
9	chr6:29717400-29719800	Weak transcription	Osteobl	bone
10	chr6:29717400-29720000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:29717400-29720000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:29717600-29719600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:29717600-29719600	Weak transcription	Hela-S3	cervix
14	chr6:29717600-29719800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:29717600-29719800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:29717600-29719800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:29717600-29719800	Weak transcription	Brain Anterior Caudate	brain
18	chr6:29717600-29719800	Weak transcription	Colonic Mucosa	Colon
19	chr6:29717600-29719800	Weak transcription	Psoas Muscle	Psoas
20	chr6:29717600-29719800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:29717600-29719800	Enhancers	Right Ventricle	heart
22	chr6:29717600-29719800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:29717600-29719800	Weak transcription	Stomach Mucosa	stomach
24	chr6:29717600-29719800	Weak transcription	NHEK	skin
25	chr6:29717600-29720000	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:29717600-29720200	Weak transcription	Gastric	stomach
27	chr6:29717800-29719600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:29717800-29719600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:29717800-29719600	Weak transcription	K562	blood
30	chr6:29717800-29719800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:29717800-29719800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:29717800-29719800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:29717800-29719800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:29717800-29719800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:29717800-29719800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:29717800-29719800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:29717800-29719800	Weak transcription	Pancreas	Pancrea
38	chr6:29717800-29720000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:29717800-29720000	Weak transcription	Brain Angular Gyrus	brain
40	chr6:29717800-29720000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:29717800-29720200	Weak transcription	Brain Substantia Nigra	brain
42	chr6:29717800-29720400	Weak transcription	Fetal Heart	heart
43	chr6:29717800-29721200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:29718000-29719600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr6:29718000-29719600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:29718000-29719600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:29718000-29719600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:29718000-29719800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr6:29718000-29719800	Weak transcription	Aorta	Aorta
50	chr6:29718000-29719800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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