Variant report

Variant	rs888995
Chromosome Location	chr19:39156138-39156139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39154116..39156228-chr19:39162782..39165101,2	K562	blood:
2	chr19:39136593..39141523-chr19:39155434..39158627,5	K562	blood:
3	chr19:39152656..39156169-chr19:39159383..39162487,4	K562	blood:
4	chr19:39153844..39156504-chr19:39338574..39341017,2	K562	blood:
5	chr19:39141727..39145361-chr19:39153035..39156463,3	K562	blood:
6	chr19:39155095..39156706-chr19:39341962..39343688,2	MCF-7	breast:
7	chr19:39154055..39157137-chr19:39203619..39206563,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11553600	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs12052046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589415	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17665451	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17708009	1.00[CHB][hapmap]
rs2228068	1.00[CHB][hapmap]
rs2368476	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41482151	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs45468197	1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4802744	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4802747	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs4802775	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs67438539	1.00[ASN][1000 genomes]
rs67953948	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258075	1.00[CHB][hapmap]
rs7258742	1.00[ASN][1000 genomes]
rs73032668	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032697	0.80[AMR][1000 genomes];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	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8103824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8182484	0.80[AMR][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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs888995	ZNF234	cis	parietal	SCAN
rs888995	LYPD3	cis	cerebellum	SCAN
rs888995	ATP1A3	cis	parietal	SCAN
rs888995	TMEM145	cis	parietal	SCAN
rs888995	KCNK6	cis	lymphoblastoid	seeQTL
rs888995	CAPN12	cis	lymphoblastoid	seeQTL
rs888995	ZNF526	cis	cerebellum	SCAN
rs888995	CAPN12	cis	multi-tissue	Pritchard
rs888995	CADM4	cis	cerebellum	SCAN
rs888995	ZC3H4	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39147800-39160800	Enhancers	Placenta	Placenta
4	chr19:39149600-39160200	Enhancers	Pancreas	Pancrea
5	chr19:39150000-39157600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
6	chr19:39151200-39157600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:39151200-39157600	Genic enhancers	Fetal Stomach	stomach
8	chr19:39151400-39156200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:39151400-39157400	Genic enhancers	NHLF	lung
10	chr19:39151400-39160000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr19:39151800-39156800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:39152000-39156200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr19:39152000-39159800	Weak transcription	Dnd41	blood
14	chr19:39152400-39159200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:39152400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:39152600-39156600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr19:39152600-39157600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:39152600-39157600	Enhancers	Fetal Lung	lung
19	chr19:39152600-39158400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:39152600-39158600	Enhancers	Ovary	ovary
21	chr19:39152600-39159200	Enhancers	Colonic Mucosa	Colon
22	chr19:39152600-39160000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:39152600-39160000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr19:39152600-39162200	Enhancers	Spleen	Spleen
25	chr19:39152600-39164000	Enhancers	Liver	Liver
26	chr19:39152800-39157000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr19:39152800-39157600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:39152800-39157600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr19:39152800-39159400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr19:39152800-39161200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:39153000-39157000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:39153000-39157200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:39153000-39157200	Enhancers	HUVEC	blood vessel
34	chr19:39153000-39158000	Enhancers	Gastric	stomach
35	chr19:39153000-39158400	Enhancers	Primary B cells from cord blood	blood
36	chr19:39153000-39158600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr19:39153000-39161200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr19:39153200-39156400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr19:39153200-39157400	Enhancers	NH-A	brain
40	chr19:39153200-39159200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:39153400-39157200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:39153400-39157400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr19:39153400-39159400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:39153400-39161200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:39153600-39156400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr19:39154000-39156200	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr19:39154000-39158800	Transcr. at gene 5' and 3'	A549	lung
48	chr19:39154000-39160200	Enhancers	Primary hematopoietic stem cells	blood
49	chr19:39154000-39160400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
50	chr19:39154000-39162600	Enhancers	Fetal Kidney	kidney

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