Variant report

Variant	rs11862813
Chromosome Location	chr16:72132356-72132357
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	chr16:71916282..71919196-chr16:72131886..72134016,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10492813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10492814	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1050361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1050362	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1050363	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12325142	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12445586	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12448315	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12708925	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12708926	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12708927	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12708928	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12924413	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12932845	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2072141	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072142	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074626	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2074627	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2240243	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2241411	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2241412	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2269918	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303285	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2550035	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2550038	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2854956	0.81[EUR][1000 genomes]
rs3764311	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764312	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3764314	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812986	0.84[ASN][1000 genomes]
rs3852781	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4788461	0.84[ASN][1000 genomes]
rs6499557	0.80[ASN][1000 genomes]
rs6499559	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6499560	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6499561	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6680	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7190995	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7191127	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7192730	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7194397	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7194668	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7200854	0.80[ASN][1000 genomes]
rs7940	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs8043606	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8047377	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8051882	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8058609	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8059378	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8059437	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8060770	0.85[ASN][1000 genomes]
rs9925763	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9926156	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9926927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9928157	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9930890	0.87[ASN][1000 genomes]
rs9932062	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9941087	0.81[EUR][1000 genomes]
rs9941346	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11862813	DHX38	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72128600-72132600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:72128800-72132600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:72128800-72136000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:72129200-72133000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr16:72129200-72133600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr16:72129200-72135000	Strong transcription	Fetal Muscle Leg	muscle
7	chr16:72129400-72133400	Weak transcription	Stomach Mucosa	stomach
8	chr16:72129400-72134000	Weak transcription	Small Intestine	intestine
9	chr16:72129400-72138800	Weak transcription	Right Atrium	heart
10	chr16:72129400-72147800	Strong transcription	Primary T cells from cord blood	blood
11	chr16:72129600-72135600	Strong transcription	Primary B cells from cord blood	blood
12	chr16:72129800-72134200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr16:72129800-72135400	Weak transcription	Fetal Heart	heart
14	chr16:72129800-72145600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr16:72129800-72146000	Strong transcription	HSMMtube	muscle
16	chr16:72129800-72146600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr16:72129800-72147000	Strong transcription	Ovary	ovary
18	chr16:72129800-72147200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr16:72129800-72147600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr16:72129800-72147800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr16:72129800-72148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr16:72129800-72149000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr16:72130000-72132400	Weak transcription	Psoas Muscle	Psoas
24	chr16:72130000-72132600	Strong transcription	HMEC	breast
25	chr16:72130000-72133000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr16:72130000-72134200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr16:72130000-72134800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr16:72130000-72135600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr16:72130000-72137000	Strong transcription	NHDF-Ad	bronchial
30	chr16:72130000-72139000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
31	chr16:72130000-72140600	Strong transcription	Fetal Kidney	kidney
32	chr16:72130000-72140600	Strong transcription	K562	blood
33	chr16:72130000-72144800	Strong transcription	Fetal Intestine Large	intestine
34	chr16:72130000-72144800	Strong transcription	Fetal Intestine Small	intestine
35	chr16:72130000-72145600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr16:72130000-72146400	Strong transcription	Colon Smooth Muscle	Colon
37	chr16:72130000-72146600	Strong transcription	HUVEC	blood vessel
38	chr16:72130000-72146800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr16:72130000-72146800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr16:72130000-72147000	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr16:72130000-72147000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr16:72130000-72147000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr16:72130000-72147000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr16:72130000-72147000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr16:72130000-72147000	Strong transcription	Esophagus	oesophagus
46	chr16:72130000-72147000	Strong transcription	NHEK	skin
47	chr16:72130000-72147200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr16:72130000-72147200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr16:72130000-72147200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr16:72130000-72147200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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