Variant report

Variant	rs855627
Chromosome Location	chr19:38613945-38613946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38611783..38614608-chr19:38870393..38872975,2	K562	blood:

Variant related genes	Relation type
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10403716	0.85[EUR][1000 genomes]
rs10405667	0.88[EUR][1000 genomes]
rs1568975	0.88[EUR][1000 genomes]
rs1614979	0.89[EUR][1000 genomes]
rs1622409	0.89[EUR][1000 genomes]
rs1625884	0.91[EUR][1000 genomes]
rs1654355	0.88[EUR][1000 genomes]
rs1654357	0.89[EUR][1000 genomes]
rs1654358	0.89[EUR][1000 genomes]
rs1654359	0.89[EUR][1000 genomes]
rs1654365	0.91[EUR][1000 genomes]
rs1654367	0.88[EUR][1000 genomes]
rs1725461	0.87[EUR][1000 genomes]
rs1725473	0.90[EUR][1000 genomes]
rs1725479	0.89[EUR][1000 genomes]
rs1725512	0.84[EUR][1000 genomes]
rs2005054	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2082442	0.91[EUR][1000 genomes]
rs2082443	0.91[EUR][1000 genomes]
rs28581256	0.95[EUR][1000 genomes]
rs3760882	0.91[EUR][1000 genomes]
rs3810356	0.91[EUR][1000 genomes]
rs4802233	0.89[EUR][1000 genomes]
rs4802239	0.91[EUR][1000 genomes]
rs4802247	0.95[EUR][1000 genomes]
rs4803786	0.97[EUR][1000 genomes]
rs4803800	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803801	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803802	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803803	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803809	0.91[EUR][1000 genomes]
rs4803810	0.91[EUR][1000 genomes]
rs56166457	0.92[EUR][1000 genomes]
rs56293547	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58152231	0.89[EUR][1000 genomes]
rs59185302	0.97[EUR][1000 genomes]
rs59579475	0.92[EUR][1000 genomes]
rs59924887	0.97[EUR][1000 genomes]
rs61388128	0.97[EUR][1000 genomes]
rs705505	0.89[EUR][1000 genomes]
rs71179415	0.90[EUR][1000 genomes]
rs7248428	0.86[EUR][1000 genomes]
rs7250034	0.91[EUR][1000 genomes]
rs729625	0.88[EUR][1000 genomes]
rs729626	0.89[EUR][1000 genomes]
rs735615	0.89[EUR][1000 genomes]
rs754123	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105468	0.97[EUR][1000 genomes]
rs8106266	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs855619	0.89[EUR][1000 genomes]
rs855621	0.89[EUR][1000 genomes]
rs855623	0.89[EUR][1000 genomes]
rs855624	0.89[EUR][1000 genomes]
rs855625	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855630	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs855631	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs855633	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855634	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855638	0.89[EUR][1000 genomes]
rs855640	0.89[EUR][1000 genomes]
rs855641	0.91[EUR][1000 genomes]
rs860623	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs863020	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs941039	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs941040	0.89[EUR][1000 genomes]
rs9941456	0.91[EUR][1000 genomes]
rs9941467	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	esv1804371	chr19:38610640-38616928	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
2	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
3	chr19:38603000-38625400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:38605800-38625400	Weak transcription	HMEC	breast
5	chr19:38608800-38614000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:38608800-38614000	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr19:38610800-38643600	Weak transcription	HepG2	liver
8	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:38611200-38625400	Weak transcription	NHEK	skin
10	chr19:38611600-38618400	Weak transcription	Brain Anterior Caudate	brain
11	chr19:38611600-38621400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:38611600-38625400	Weak transcription	Fetal Heart	heart
13	chr19:38611600-38626000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr19:38611600-38634400	Weak transcription	Stomach Mucosa	stomach
15	chr19:38611600-38634800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:38611600-38634800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:38611600-38641400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
19	chr19:38611800-38614600	Weak transcription	Psoas Muscle	Psoas
20	chr19:38611800-38623600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:38611800-38623800	Weak transcription	GM12878-XiMat	blood
22	chr19:38611800-38634600	Weak transcription	NH-A	brain
23	chr19:38611800-38642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
25	chr19:38612200-38614000	Strong transcription	A549	lung
26	chr19:38612800-38614000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chr19:38612800-38614000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
28	chr19:38612800-38614000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
29	chr19:38612800-38614000	Strong transcription	HSMM	muscle
30	chr19:38613000-38614000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr19:38613000-38614000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr19:38613000-38614000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:38613000-38614000	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr19:38613000-38614000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:38613000-38614000	ZNF genes & repeats	Fetal Brain Female	brain
36	chr19:38613200-38614000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
37	chr19:38613400-38614000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr19:38613400-38633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:38613400-38634400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr19:38613600-38614000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr19:38613600-38620800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:38613600-38625600	Weak transcription	Hela-S3	cervix
43	chr19:38613600-38634800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr19:38613800-38614000	Enhancers	K562	blood
45	chr19:38613800-38615400	Weak transcription	Fetal Intestine Large	intestine
46	chr19:38613800-38615600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:38613800-38615600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:38613800-38615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:38613800-38615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:38613800-38615600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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