Variant report

Variant	rs67953948
Chromosome Location	chr19:39170029-39170030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39169983..39173495-chr19:39173704..39177059,4	K562	blood:
2	chr19:39169995..39171948-chr19:39172735..39174419,2	MCF-7	breast:
3	chr19:39138054..39139945-chr19:39169569..39171222,2	K562	blood:
4	chr19:39145322..39147138-chr19:39167386..39170239,2	K562	blood:
5	chr19:39140553..39142565-chr19:39169330..39171049,2	MCF-7	breast:
6	chr19:39124852..39127091-chr19:39168674..39171313,2	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11553600	1.00[ASN][1000 genomes]
rs12052046	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589415	1.00[ASN][1000 genomes]
rs17665451	1.00[ASN][1000 genomes]
rs2368476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41482151	1.00[ASN][1000 genomes]
rs45468197	1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4802744	1.00[ASN][1000 genomes]
rs4802747	1.00[ASN][1000 genomes]
rs4802775	1.00[ASN][1000 genomes]
rs67438539	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7258742	1.00[ASN][1000 genomes]
rs73032668	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032691	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032697	1.00[ASN][1000 genomes]
rs73034621	1.00[ASN][1000 genomes]
rs73038909	1.00[ASN][1000 genomes]
rs73038918	1.00[ASN][1000 genomes]
rs73038924	1.00[ASN][1000 genomes]
rs73038930	1.00[ASN][1000 genomes]
rs73038936	1.00[ASN][1000 genomes]
rs73038948	1.00[ASN][1000 genomes]
rs7351086	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8103824	1.00[ASN][1000 genomes]
rs8182484	1.00[ASN][1000 genomes]
rs888995	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39160400-39173400	Weak transcription	Brain Germinal Matrix	brain
2	chr19:39161200-39176000	Weak transcription	Fetal Brain Male	brain
3	chr19:39161200-39176000	Weak transcription	Fetal Brain Female	brain
4	chr19:39162200-39173400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:39162400-39172000	Enhancers	Left Ventricle	heart
6	chr19:39162800-39173200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:39164400-39172600	Enhancers	Small Intestine	intestine
8	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
9	chr19:39164600-39170400	Enhancers	Right Atrium	heart
10	chr19:39164600-39170800	Genic enhancers	Osteobl	bone
11	chr19:39164600-39173800	Genic enhancers	HepG2	liver
12	chr19:39164600-39178200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr19:39164800-39170200	Genic enhancers	Rectal Mucosa Donor 29	rectum
14	chr19:39164800-39170600	Enhancers	Primary B cells from peripheral blood	blood
15	chr19:39164800-39170800	Enhancers	Brain Hippocampus Middle	brain
16	chr19:39164800-39170800	Enhancers	Psoas Muscle	Psoas
17	chr19:39164800-39171000	Genic enhancers	Rectal Mucosa Donor 31	rectum
18	chr19:39164800-39171400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:39164800-39172600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr19:39164800-39173800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:39164800-39177600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr19:39164800-39179200	Enhancers	Pancreas	Pancrea
23	chr19:39164800-39179800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:39165000-39174200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr19:39165200-39171800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:39165400-39172000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
28	chr19:39165400-39172600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr19:39165400-39178200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:39165600-39171200	Enhancers	GM12878-XiMat	blood
31	chr19:39165600-39172000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr19:39165600-39174000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:39166000-39178200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:39166200-39172400	Genic enhancers	NHEK	skin
35	chr19:39166200-39173800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:39166200-39173800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:39166400-39173800	Genic enhancers	HMEC	breast
38	chr19:39166600-39171200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:39166600-39173400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:39166800-39170200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:39167200-39170200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr19:39167200-39171800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr19:39167200-39173600	Enhancers	Stomach Mucosa	stomach
44	chr19:39167200-39173800	Genic enhancers	Fetal Intestine Large	intestine
45	chr19:39167200-39175600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr19:39167400-39173600	Genic enhancers	Lung	lung
47	chr19:39167400-39173800	Genic enhancers	NHLF	lung
48	chr19:39167400-39174400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:39167400-39180800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:39167600-39170400	Genic enhancers	Brain Substantia Nigra	brain

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