Variant report

Variant	rs3817826
Chromosome Location	chr6:29696118-29696119
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr6:29695785-29699667	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:29695736-29696450	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:29690658-29699867	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:29695149-29697426	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:29695427-29697285	GM15510	blood:	n/a	n/a
6	RUNX3	chr6:29695939-29696399	GM12878	blood:	n/a	n/a
7	PML	chr6:29695415-29699000	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:29695188-29697002	GM12891	blood:	n/a	n/a
9	POLR2A	chr6:29695131-29697353	GM12891	blood:	n/a	n/a
10	POLR2A	chr6:29695163-29699574	GM19099	blood:	n/a	n/a
11	POLR2A	chr6:29694623-29699123	GM12892	blood:	n/a	n/a
12	MTA3	chr6:29695276-29699589	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:29695304-29697234	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:29690785-29699707	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:29695342-29697252	GM19193	blood:	n/a	n/a
16	POLR2A	chr6:29690681-29699847	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:29690708-29699614	GM18505	blood:	n/a	n/a
18	STAT5A	chr6:29695345-29696882	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:29690566-29699452	GM12892	blood:	n/a	n/a
20	NFATC1	chr6:29695654-29699504	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:29690657-29697457	GM12892	blood:	n/a	n/a
22	POU2F2	chr6:29695816-29696339	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:29695365-29699302	GM18526	blood:	n/a	n/a
24	POLR2A	chr6:29690618-29699456	GM12892	blood:	n/a	n/a
25	POLR2A	chr6:29690594-29697494	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:29695198-29698947	GM12891	blood:	n/a	n/a
27	POLR2A	chr6:29695079-29697466	GM12892	blood:	n/a	n/a
28	POLR2A	chr6:29695038-29699514	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:29695318-29696429	GM12878	blood:	n/a	n/a
30	BCLAF1	chr6:29695785-29696868	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:29695270-29699448	GM18951	blood:	n/a	n/a
32	MTA3	chr6:29696073-29696518	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:29695318-29697307	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29691971..29693668-chr6:29693958..29696725,2	K562	blood:
2	chr6:29689319..29693460-chr6:29694038..29698697,5	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MOG-2	chr6:29695734-29697128	NONHSAT108542

No data

Variant related genes	Relation type
RPL23AP1	TF binding region
HCG4P11	TF binding region
ENSG00000204642	Chromatin interaction
ENSG00000225864	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1736919	0.83[ASN][1000 genomes]
rs2072894	0.85[ASN][1000 genomes]
rs2072896	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2075682	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2076174	0.85[ASN][1000 genomes]
rs2272874	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3734813	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3734815	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736694	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736697	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757324	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757325	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757326	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3823318	0.84[ASN][1000 genomes]
rs6901686	0.85[ASN][1000 genomes]
rs6910733	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7738786	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7739360	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7739388	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7741597	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7742523	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7751815	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7753946	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7754692	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755571	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759272	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7773358	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9258156	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9258158	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258160	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258163	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258164	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258166	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258167	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258168	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258169	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258170	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258171	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258172	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258173	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258174	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258175	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258176	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9258187	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258192	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258203	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258205	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258207	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258211	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258212	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258214	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258215	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258216	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9258218	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258223	0.81[ASN][1000 genomes]
rs9258224	0.84[ASN][1000 genomes]
rs9258225	0.85[ASN][1000 genomes]
rs9258226	0.81[ASN][1000 genomes]
rs9258227	0.81[ASN][1000 genomes]
rs9258230	0.85[ASN][1000 genomes]
rs9258236	0.85[ASN][1000 genomes]
rs9258241	0.88[ASN][1000 genomes]
rs9258242	0.85[ASN][1000 genomes]
rs9258244	0.84[ASN][1000 genomes]
rs9258258	0.84[ASN][1000 genomes]
rs9258259	0.84[ASN][1000 genomes]
rs9258260	0.84[ASN][1000 genomes]
rs9258262	0.84[ASN][1000 genomes]
rs9258265	0.84[ASN][1000 genomes]
rs9258272	0.85[ASN][1000 genomes]
rs9258274	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv462673	chr6:29689590-29700183	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv601230	chr6:29689590-29700183	Flanking Active TSS Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv883531	chr6:29692562-29705402	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3817826	HLA-F	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29692200-29701800	Weak transcription	HMEC	breast
2	chr6:29692200-29715800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:29692600-29696200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:29692600-29696400	Genic enhancers	Spleen	Spleen
6	chr6:29692600-29697400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:29693200-29696200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
10	chr6:29693400-29697000	Weak transcription	Fetal Thymus	thymus
11	chr6:29693400-29700000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
13	chr6:29693600-29696200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:29693600-29696800	Weak transcription	Fetal Intestine Large	intestine
15	chr6:29693600-29697600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:29693600-29715600	Weak transcription	NHLF	lung
17	chr6:29693800-29696400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:29693800-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
21	chr6:29694000-29696200	Strong transcription	Adipose Nuclei	Adipose
22	chr6:29694000-29696200	Strong transcription	Liver	Liver
23	chr6:29694000-29696200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:29694000-29696400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:29694000-29696400	Strong transcription	Lung	lung
26	chr6:29694000-29696400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:29694000-29696400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr6:29694000-29696600	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr6:29694000-29696600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:29694000-29696600	Strong transcription	Brain Anterior Caudate	brain
31	chr6:29694000-29696600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr6:29694000-29696800	Strong transcription	Colonic Mucosa	Colon
33	chr6:29694000-29707000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:29694000-29711400	Weak transcription	Gastric	stomach
36	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
37	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:29694200-29696200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:29694200-29696200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:29694200-29696200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:29694200-29696200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr6:29694200-29696200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr6:29694200-29696400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:29694200-29696400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr6:29694200-29696400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:29694200-29696800	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr6:29694200-29696800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:29694200-29697000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:29694200-29701800	Weak transcription	NHEK	skin
50	chr6:29694200-29705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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