Variant report

Variant	rs41300510
Chromosome Location	chr1:84630507-84630508
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	YY1	chr1:84630184-84630725	SK-N-SH	brain:	n/a	chr1:84630377-84630385 chr1:84630374-84630384
2	POLR2A	chr1:84629799-84630862	H1-neurons	neurons:	n/a	n/a
3	YY1	chr1:84630193-84630588	SK-N-SH_RA	brain:	n/a	chr1:84630377-84630385 chr1:84630374-84630384
4	POLR2A	chr1:84629702-84630831	H1-neurons	neurons:	n/a	n/a
5	TAF1	chr1:84629797-84630606	H1-neurons	neurons:	n/a	n/a
6	REST	chr1:84629052-84635293	H1-neurons	neurons:	n/a	n/a
7	REST	chr1:84629811-84630735	H1-neurons	neurons:	n/a	n/a
8	RFX5	chr1:84629103-84630995	SK-N-SH	brain:	n/a	chr1:84630303-84630318 chr1:84630302-84630319 chr1:84630303-84630318 chr1:84630303-84630318
9	TAF1	chr1:84629874-84630765	H1-neurons	neurons:	n/a	n/a
10	YY1	chr1:84630182-84630536	SK-N-SH_RA	brain:	n/a	chr1:84630377-84630385 chr1:84630374-84630384

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SAMD13-1	chr1:84630387-84630696	NONHSAT004188

Variant related genes	Relation type
PRKACB	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs3729862	1.00[AFR][1000 genomes]
rs41301144	1.00[AFR][1000 genomes]
rs41301146	1.00[AFR][1000 genomes]
rs58384983	0.86[AFR][1000 genomes]
rs7513220	0.86[AFR][1000 genomes]
rs7530485	1.00[AFR][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	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv546690	chr1:84562265-84655238	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv871731	chr1:84597396-84658591	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv871656	chr1:84601048-84693671	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv997601	chr1:84609346-84672859	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1005225	chr1:84609871-84667950	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1002537	chr1:84611207-84658450	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv999772	chr1:84611207-84667218	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1013911	chr1:84619164-84667950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv871375	chr1:84622793-84678418	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv871643	chr1:84628655-84705481	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84610400-84633400	Weak transcription	Fetal Kidney	kidney
2	chr1:84614000-84633800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:84615800-84634800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:84616200-84635200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:84622400-84635800	Weak transcription	Small Intestine	intestine
6	chr1:84623000-84639200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:84624000-84651800	Weak transcription	Thymus	Thymus
8	chr1:84624200-84630800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:84624800-84633200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:84625600-84635600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:84625800-84634000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:84627200-84631000	Weak transcription	HUVEC	blood vessel
13	chr1:84627600-84635400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:84628800-84630600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:84629200-84636400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:84629200-84654000	Weak transcription	Spleen	Spleen
17	chr1:84629400-84630600	Active TSS	NHDF-Ad	bronchial
18	chr1:84629400-84632800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:84629400-84644400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:84629600-84630600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:84629600-84630600	Active TSS	Osteobl	bone
22	chr1:84629600-84632400	Active TSS	Brain Angular Gyrus	brain
23	chr1:84629600-84632800	Active TSS	Brain Cingulate Gyrus	brain
24	chr1:84629600-84633000	Active TSS	Brain Germinal Matrix	brain
25	chr1:84629600-84633000	Active TSS	Brain Hippocampus Middle	brain
26	chr1:84629600-84633800	Active TSS	Brain Anterior Caudate	brain
27	chr1:84629600-84634000	Active TSS	Fetal Brain Female	brain
28	chr1:84629800-84630600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:84629800-84630600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:84629800-84630600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:84629800-84630600	Active TSS	Fetal Muscle Trunk	muscle
32	chr1:84629800-84630600	Active TSS	Fetal Stomach	stomach
33	chr1:84629800-84630600	Active TSS	Right Atrium	heart
34	chr1:84629800-84630600	Active TSS	NH-A	brain
35	chr1:84629800-84630600	Active TSS	NHLF	lung
36	chr1:84629800-84630800	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:84629800-84630800	Active TSS	Ovary	ovary
38	chr1:84629800-84631400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:84629800-84632000	Active TSS	Brain Substantia Nigra	brain
40	chr1:84629800-84632000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr1:84629800-84632200	Active TSS	Fetal Brain Male	brain
42	chr1:84629800-84632800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:84629800-84633000	Enhancers	Primary B cells from peripheral blood	blood
44	chr1:84629800-84633200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:84630000-84630600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr1:84630000-84630600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:84630000-84630600	Active TSS	Fetal Muscle Leg	muscle
48	chr1:84630000-84630800	Active TSS	Primary T cells fromperipheralblood	blood
49	chr1:84630000-84631000	Enhancers	Primary hematopoietic stem cells	blood
50	chr1:84630200-84630600	Enhancers	Adipose Nuclei	Adipose

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