Variant report

Variant	rs41300514
Chromosome Location	chr1:84631536-84631537
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11163916	1.00[EUR][1000 genomes]
rs11802352	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11802582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11803089	1.00[EUR][1000 genomes]
rs11810469	1.00[AMR][1000 genomes]
rs3729868	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41300502	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41300516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41300534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41301174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs624878	1.00[EUR][1000 genomes]
rs633253	1.00[EUR][1000 genomes]
rs639010	1.00[EUR][1000 genomes]
rs639940	1.00[EUR][1000 genomes]
rs642052	1.00[EUR][1000 genomes]
rs652426	1.00[EUR][1000 genomes]
rs655181	1.00[EUR][1000 genomes]
rs7524666	1.00[EUR][1000 genomes]
rs7524960	1.00[EUR][1000 genomes]
rs7532830	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7533541	1.00[EUR][1000 genomes]
rs7538094	1.00[EUR][1000 genomes]
rs7540972	1.00[EUR][1000 genomes]
rs7547471	0.87[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:47 , 50 per page) page: 1

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	chr1:84624800-84633200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:84625600-84635600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:84625800-84634000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:84627600-84635400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:84629200-84636400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr1:84629200-84654000	Weak transcription	Spleen	Spleen
14	chr1:84629400-84632800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:84629400-84644400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:84629600-84632400	Active TSS	Brain Angular Gyrus	brain
17	chr1:84629600-84632800	Active TSS	Brain Cingulate Gyrus	brain
18	chr1:84629600-84633000	Active TSS	Brain Germinal Matrix	brain
19	chr1:84629600-84633000	Active TSS	Brain Hippocampus Middle	brain
20	chr1:84629600-84633800	Active TSS	Brain Anterior Caudate	brain
21	chr1:84629600-84634000	Active TSS	Fetal Brain Female	brain
22	chr1:84629800-84632000	Active TSS	Brain Substantia Nigra	brain
23	chr1:84629800-84632000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:84629800-84632200	Active TSS	Fetal Brain Male	brain
25	chr1:84629800-84632800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:84629800-84633000	Enhancers	Primary B cells from peripheral blood	blood
27	chr1:84629800-84633200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr1:84630200-84631600	Enhancers	Colon Smooth Muscle	Colon
29	chr1:84630200-84632200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:84630200-84634200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr1:84630400-84633000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:84630600-84632600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:84630600-84633800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:84630600-84635200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr1:84630600-84639800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:84630600-84640400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:84630800-84632600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr1:84630800-84633800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:84630800-84648200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:84631000-84632200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:84631000-84632600	Enhancers	HUVEC	blood vessel
42	chr1:84631000-84636400	Enhancers	Primary T cells from cord blood	blood
43	chr1:84631200-84631800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:84631200-84633800	Weak transcription	Primary B cells from cord blood	blood
45	chr1:84631400-84631600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr1:84631400-84632800	Enhancers	Dnd41	blood
47	chr1:84631400-84633000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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