Variant report

Variant	rs34754809
Chromosome Location	chr19:39033180-39033181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39033172..39036412-chr19:39037332..39039835,4	K562	blood:
2	chr19:39033172..39035020-chr19:39038093..39039805,2	K562	blood:
3	chr19:39026149..39027829-chr19:39031643..39034641,2	K562	blood:
4	chr19:39029247..39031179-chr19:39031393..39034071,2	MCF-7	breast:
5	chr19:39033166..39035444-chr19:39222579..39224639,2	K562	blood:
6	chr19:39028747..39031280-chr19:39032458..39034855,3	K562	blood:

Variant related genes	Relation type
ENSG00000268055	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1004795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415792	0.88[EUR][1000 genomes]
rs12459024	1.00[ASN][1000 genomes]
rs12459749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984412	1.00[ASN][1000 genomes]
rs2292797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960350	1.00[ASN][1000 genomes]
rs3786830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829976	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs45613041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802589	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802608	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv1058902	chr19:39025940-39078574	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1064490	chr19:39029788-39078574	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38960800-39034400	Strong transcription	Skeletal Muscle Female	skeletal muscle
2	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
3	chr19:39026000-39052400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:39026400-39034200	Weak transcription	Brain Substantia Nigra	brain
5	chr19:39026400-39034400	Weak transcription	Brain Angular Gyrus	brain
6	chr19:39026400-39034800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:39026600-39034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:39026600-39034400	Weak transcription	Brain Anterior Caudate	brain
9	chr19:39026600-39034400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:39026600-39034400	Weak transcription	Brain Hippocampus Middle	brain
11	chr19:39026600-39034400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:39026600-39034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:39026600-39034800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr19:39027800-39034200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr19:39028200-39034200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:39028400-39035200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:39028600-39034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:39028600-39034800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr19:39029000-39051600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr19:39029200-39034400	Weak transcription	Esophagus	oesophagus
21	chr19:39029200-39034400	Weak transcription	Pancreas	Pancrea
22	chr19:39029600-39046000	Weak transcription	HSMM	muscle
23	chr19:39029800-39034600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr19:39029800-39035000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:39029800-39035200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:39030000-39034200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:39030000-39034200	Weak transcription	HMEC	breast
28	chr19:39030000-39035200	Weak transcription	Primary T cells from cord blood	blood
29	chr19:39030000-39054600	Strong transcription	Fetal Muscle Leg	muscle
30	chr19:39030200-39034400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr19:39030200-39034600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:39030200-39034800	Weak transcription	Stomach Mucosa	stomach
33	chr19:39030200-39035200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:39030200-39055200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:39030400-39035000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:39030600-39034000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr19:39030600-39034200	Weak transcription	Adipose Nuclei	Adipose
38	chr19:39030600-39034600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr19:39030600-39034800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:39030800-39034600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr19:39030800-39034600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:39030800-39034600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:39030800-39034800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:39030800-39034800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr19:39031800-39034600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:39032000-39034600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:39032200-39033600	Weak transcription	HSMMtube	muscle
48	chr19:39033000-39033600	Weak transcription	K562	blood
49	chr19:39033000-39033800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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