Variant report

Variant	rs855633
Chromosome Location	chr19:38606515-38606516
allele	C/G
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	POLR2A	chr19:38605793-38606733	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104313838..104315434-chr19:38606255..38607755,2	MCF-7	breast:

Variant related genes	Relation type
SIPA1L3	TF binding region
ENSG00000258735	Chromatin interaction
ENSG00000088808	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10403716	0.84[EUR][1000 genomes]
rs10405667	0.89[EUR][1000 genomes]
rs10412762	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs10420506	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs10422665	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs1568975	0.89[EUR][1000 genomes]
rs1614979	0.94[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs1622409	0.90[EUR][1000 genomes]
rs1625884	0.92[EUR][1000 genomes]
rs1654355	0.89[EUR][1000 genomes]
rs1654357	0.90[EUR][1000 genomes]
rs1654358	0.90[EUR][1000 genomes]
rs1654359	0.90[EUR][1000 genomes]
rs1654365	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1654367	0.89[EUR][1000 genomes]
rs1725461	0.88[EUR][1000 genomes]
rs1725473	0.91[EUR][1000 genomes]
rs1725479	0.90[EUR][1000 genomes]
rs1725512	0.94[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs2005054	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2082442	0.90[EUR][1000 genomes]
rs2082443	0.90[EUR][1000 genomes]
rs28412601	0.80[EUR][1000 genomes]
rs28581256	0.94[EUR][1000 genomes]
rs3760882	0.92[EUR][1000 genomes]
rs3810356	0.92[EUR][1000 genomes]
rs4802233	0.94[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs4802239	0.92[EUR][1000 genomes]
rs4802247	0.94[EUR][1000 genomes]
rs4802256	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs4802278	0.81[CHB][hapmap]
rs4803786	0.96[EUR][1000 genomes]
rs4803800	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803801	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803802	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803803	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803809	0.90[EUR][1000 genomes]
rs4803810	0.90[EUR][1000 genomes]
rs4803828	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs4803829	0.91[CHB][hapmap]
rs4803862	0.81[CHB][hapmap]
rs56166457	0.93[EUR][1000 genomes]
rs56293547	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58152231	0.90[EUR][1000 genomes]
rs59185302	0.96[EUR][1000 genomes]
rs59579475	0.93[EUR][1000 genomes]
rs59924887	0.96[EUR][1000 genomes]
rs61388128	0.96[EUR][1000 genomes]
rs705505	0.90[EUR][1000 genomes]
rs71179415	0.89[EUR][1000 genomes]
rs7248428	0.85[EUR][1000 genomes]
rs7250034	0.90[EUR][1000 genomes]
rs729625	0.89[EUR][1000 genomes]
rs729626	0.90[EUR][1000 genomes]
rs735615	0.90[EUR][1000 genomes]
rs754123	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105468	0.96[EUR][1000 genomes]
rs8106266	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs855603	0.94[CEU][hapmap]
rs855619	0.90[EUR][1000 genomes]
rs855621	0.90[EUR][1000 genomes]
rs855623	0.90[EUR][1000 genomes]
rs855624	0.90[EUR][1000 genomes]
rs855625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855627	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855630	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855631	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs855634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855638	0.90[EUR][1000 genomes]
rs855640	0.90[EUR][1000 genomes]
rs855641	0.92[EUR][1000 genomes]
rs860623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941040	0.94[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs9941456	0.90[EUR][1000 genomes]
rs9941467	0.94[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
3	chr19:38581600-38610000	Weak transcription	Psoas Muscle	Psoas
4	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr19:38588800-38606600	Strong transcription	Liver	Liver
7	chr19:38589200-38606800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr19:38590200-38606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:38590200-38606600	Strong transcription	Stomach Smooth Muscle	stomach
10	chr19:38590200-38611000	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr19:38590400-38609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr19:38590800-38606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:38590800-38608800	Strong transcription	Fetal Intestine Small	intestine
14	chr19:38591800-38609000	Strong transcription	Fetal Stomach	stomach
15	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
16	chr19:38594400-38606800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr19:38594600-38606800	Strong transcription	GM12878-XiMat	blood
18	chr19:38595800-38606600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:38596000-38610000	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:38596000-38613800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:38596200-38606600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:38597800-38606600	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr19:38597800-38610200	Weak transcription	HUVEC	blood vessel
24	chr19:38597800-38611800	Strong transcription	Osteobl	bone
25	chr19:38597800-38612000	Strong transcription	HSMM	muscle
26	chr19:38598000-38610200	Strong transcription	A549	lung
27	chr19:38598200-38611800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:38598800-38606600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:38599800-38606600	Strong transcription	HSMMtube	muscle
30	chr19:38600200-38606800	Strong transcription	Brain Hippocampus Middle	brain
31	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
32	chr19:38601200-38608000	Weak transcription	Left Ventricle	heart
33	chr19:38602800-38606800	Strong transcription	Gastric	stomach
34	chr19:38602800-38612800	Weak transcription	Hela-S3	cervix
35	chr19:38603000-38607600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:38603000-38607600	Weak transcription	HepG2	liver
37	chr19:38603000-38608400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:38603000-38608600	Weak transcription	Fetal Lung	lung
39	chr19:38603000-38609400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr19:38603000-38609400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr19:38603000-38609800	Weak transcription	Stomach Mucosa	stomach
42	chr19:38603000-38609800	Weak transcription	NHLF	lung
43	chr19:38603000-38610000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:38603000-38610000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr19:38603000-38610000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr19:38603000-38610000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:38603000-38610000	Weak transcription	Brain Anterior Caudate	brain
48	chr19:38603000-38610000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:38603000-38610000	Weak transcription	Esophagus	oesophagus
50	chr19:38603000-38610000	Weak transcription	Placenta Amnion	Placenta Amnion

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