Variant report

Variant	rs2195453
Chromosome Location	chr19:21312910-21312911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21312896..21314771-chr19:21323680..21326350,2	K562	blood:

Variant related genes	Relation type
ENSG00000196705	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10164375	0.86[ASN][1000 genomes]
rs10401931	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10403266	0.83[ASN][1000 genomes]
rs10405180	0.97[ASN][1000 genomes]
rs10405218	0.85[ASN][1000 genomes]
rs10405406	0.91[ASN][1000 genomes]
rs10406661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs10408496	0.81[JPT][hapmap]
rs10409844	0.85[ASN][1000 genomes]
rs10409877	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10410901	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10411038	0.91[ASN][1000 genomes]
rs10412267	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs10412509	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs10413175	0.88[ASN][1000 genomes]
rs10413983	0.88[ASN][1000 genomes]
rs10414134	0.88[ASN][1000 genomes]
rs10421819	0.86[ASN][1000 genomes]
rs10422193	0.81[ASN][1000 genomes]
rs10423541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10424283	0.88[ASN][1000 genomes]
rs10425969	0.85[ASN][1000 genomes]
rs11085431	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11666640	0.85[ASN][1000 genomes]
rs11666869	0.94[ASN][1000 genomes]
rs11667674	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668952	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668985	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670162	0.88[ASN][1000 genomes]
rs11671397	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672142	0.85[ASN][1000 genomes]
rs11672727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878599	1.00[ASN][1000 genomes]
rs12104220	0.88[ASN][1000 genomes]
rs12609005	0.85[ASN][1000 genomes]
rs12609167	0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12609427	0.90[ASN][1000 genomes]
rs12973640	0.88[ASN][1000 genomes]
rs12973921	1.00[ASN][1000 genomes]
rs12974016	0.91[ASN][1000 genomes]
rs12981855	0.86[ASN][1000 genomes]
rs1470021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1470022	0.94[ASN][1000 genomes]
rs1609441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1968523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs2013048	0.88[ASN][1000 genomes]
rs2082003	0.88[ASN][1000 genomes]
rs2115493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2115494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115495	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115496	0.94[JPT][hapmap];0.95[YRI][hapmap];0.80[ASN][1000 genomes]
rs2164988	0.80[ASN][1000 genomes]
rs2164989	0.85[ASN][1000 genomes]
rs2195454	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]
rs2358803	1.00[ASN][1000 genomes]
rs2358804	1.00[ASN][1000 genomes]
rs2884554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35137761	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4488591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4808275	0.91[ASN][1000 genomes]
rs4808276	1.00[ASN][1000 genomes]
rs4809119	0.82[ASN][1000 genomes]
rs4809122	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs6511183	0.85[ASN][1000 genomes]
rs6511184	0.85[ASN][1000 genomes]
rs6511186	0.88[ASN][1000 genomes]
rs6511187	0.82[ASN][1000 genomes]
rs6511188	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6511190	0.80[ASN][1000 genomes]
rs6511191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6511192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6511194	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6511195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6511196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6511198	1.00[ASN][1000 genomes]
rs6511199	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511200	1.00[ASN][1000 genomes]
rs6511201	1.00[ASN][1000 genomes]
rs7246723	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7248410	0.91[ASN][1000 genomes]
rs7249283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7249736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7250169	0.88[ASN][1000 genomes]
rs7253950	0.94[ASN][1000 genomes]
rs7254047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7254053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7254982	0.86[ASN][1000 genomes]
rs7257481	0.88[ASN][1000 genomes]
rs7258195	0.88[ASN][1000 genomes]
rs7258409	0.88[ASN][1000 genomes]
rs7260268	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7260600	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs7343175	0.94[ASN][1000 genomes]
rs741674	0.94[ASN][1000 genomes]
rs741676	0.94[ASN][1000 genomes]
rs8100289	0.91[ASN][1000 genomes]
rs8100599	0.88[ASN][1000 genomes]
rs8101222	0.97[ASN][1000 genomes]
rs8101412	0.88[ASN][1000 genomes]
rs8101461	0.97[ASN][1000 genomes]
rs8103825	0.91[ASN][1000 genomes]
rs8106801	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8106923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8107638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8107982	0.85[ASN][1000 genomes]
rs8109549	0.92[ASN][1000 genomes]
rs8111827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs8112054	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8112216	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8112500	0.91[ASN][1000 genomes]
rs8113541	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8182465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9304980	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9304981	0.93[JPT][hapmap]
rs9304982	0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs9967619	0.81[JPT][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1065384	chr19:21249321-21350698	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv911413	chr19:21263518-21347598	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3319019	chr19:21268262-21336383	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3319020	chr19:21268262-21336383	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	esv7695	chr19:21268276-21328430	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	esv5909	chr19:21272333-21334753	Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	esv3420290	chr19:21272477-21336432	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	esv3391713	chr19:21272485-21334631	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	esv5243	chr19:21272548-21334670	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	esv7204	chr19:21274198-21336396	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
16	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
17	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2195453	HAPLN4	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21304200-21313000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr19:21305800-21313000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:21305800-21313000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:21309400-21313400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr19:21310600-21313000	Enhancers	Fetal Intestine Large	intestine
6	chr19:21311200-21313400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr19:21311600-21313000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr19:21312000-21314200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr19:21312400-21313000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:21312400-21313000	Weak transcription	HepG2	liver
11	chr19:21312400-21313000	Enhancers	K562	blood
12	chr19:21312400-21313400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:21312400-21313800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:21312600-21313200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:21312600-21313200	Weak transcription	Pancreas	Pancrea
16	chr19:21312800-21313000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:21312800-21313400	Enhancers	HUES64 Cell Line	embryonic stem cell

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