Variant report

Variant	rs30454
Chromosome Location	chr19:39844176-39844177
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	chr19:39840535..39845164-chr19:39896257..39899085,6	K562	blood:
2	chr19:39843827..39847459-chr19:39858082..39862141,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128016	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000241983	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1375910	0.91[JPT][hapmap]
rs16973342	0.91[JPT][hapmap]
rs16973348	0.91[JPT][hapmap]
rs16973350	0.91[JPT][hapmap]
rs16973363	0.91[JPT][hapmap]
rs16973374	0.90[JPT][hapmap]
rs194016	0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs2067102	0.91[JPT][hapmap]
rs2074852	0.91[JPT][hapmap]
rs251905	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs251906	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs251907	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28370340	0.81[ASN][1000 genomes]
rs28668750	0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs30453	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30458	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34615060	0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs36264	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36266	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36270	1.00[ASW][hapmap];0.93[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786949	0.91[JPT][hapmap]
rs3826938	0.90[JPT][hapmap]
rs3865515	0.91[JPT][hapmap]
rs40353	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs40441	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45601936	0.81[ASN][1000 genomes]
rs562638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508860	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs685125	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7246750	0.81[ASN][1000 genomes]
rs7250420	0.81[ASN][1000 genomes]
rs8102194	0.81[ASN][1000 genomes]
rs917319	1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
5	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
8	nsv520245	chr19:39844176-39850102	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834200-39846600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:39834400-39844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:39834400-39845400	Weak transcription	Fetal Kidney	kidney
5	chr19:39834400-39849200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:39834800-39847400	Weak transcription	Small Intestine	intestine
7	chr19:39834800-39852800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:39834800-39852800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:39835000-39844600	Weak transcription	Stomach Mucosa	stomach
11	chr19:39835000-39846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:39835600-39853600	Strong transcription	Placenta	Placenta
13	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr19:39836000-39847600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
17	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr19:39836600-39845600	Weak transcription	Aorta	Aorta
19	chr19:39836600-39845800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
23	chr19:39836800-39846000	Weak transcription	Pancreas	Pancrea
24	chr19:39836800-39852000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:39836800-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:39837400-39846400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:39837600-39863600	Strong transcription	Fetal Intestine Small	intestine
29	chr19:39837800-39854400	Strong transcription	Fetal Stomach	stomach
30	chr19:39837800-39855400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:39838000-39851800	Strong transcription	Liver	Liver
32	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
33	chr19:39838200-39858200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:39838200-39858200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:39838200-39862600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr19:39838400-39853200	Strong transcription	A549	lung
37	chr19:39838600-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:39838800-39845800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:39839000-39857600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr19:39839000-39858200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:39839200-39846000	Weak transcription	Right Ventricle	heart
44	chr19:39839200-39851800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:39839200-39852600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:39839200-39853400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:39839200-39879200	Strong transcription	Dnd41	blood
48	chr19:39839800-39847400	Weak transcription	Fetal Heart	heart
49	chr19:39840000-39844600	Weak transcription	Hela-S3	cervix
50	chr19:39841000-39852600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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