Variant report

Variant	rs7940
Chromosome Location	chr16:72146441-72146442
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:72143268..72145406-chr16:72145794..72147509,2	MCF-7	breast:
2	chr16:72144522..72146740-chr16:72151105..72152934,2	K562	blood:
3	chr16:71879780..71881511-chr16:72144276..72147011,2	MCF-7	breast:
4	chr16:72138442..72141132-chr16:72144347..72146583,2	K562	blood:
5	chr16:72137539..72141132-chr16:72143530..72146583,3	K562	blood:
6	chr16:72139817..72142813-chr16:72144026..72146841,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140829	Chromatin interaction
ENSG00000224470	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10400963	0.91[JPT][hapmap]
rs10492813	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs10492814	0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs1050361	0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1050362	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs1050363	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10852511	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11075924	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11643192	0.85[JPT][hapmap]
rs11862813	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12162087	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12325142	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs12325266	0.86[JPT][hapmap]
rs12443622	0.81[ASN][1000 genomes]
rs12449073	0.91[JPT][hapmap];0.84[YRI][hapmap]
rs12708925	0.89[ASN][1000 genomes]
rs12708928	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs12917999	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12924413	0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs12928365	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12930702	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12932845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12935266	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs1465457	0.94[YRI][hapmap]
rs16973716	0.95[JPT][hapmap]
rs2070937	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2070939	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap]
rs2072141	0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2072142	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs2074626	0.85[JPT][hapmap];0.81[YRI][hapmap]
rs2074627	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs217181	1.00[YRI][hapmap]
rs2236765	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240243	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs2241411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241412	0.81[JPT][hapmap];0.86[YRI][hapmap]
rs2269918	0.89[ASN][1000 genomes]
rs2288000	0.86[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs2288002	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2303285	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs251033	0.82[ASN][1000 genomes]
rs2550035	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2550038	0.87[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.83[ASN][1000 genomes]
rs2550868	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2550869	0.82[ASN][1000 genomes]
rs2550870	0.82[ASN][1000 genomes]
rs2550876	0.81[ASN][1000 genomes]
rs2854956	0.82[JPT][hapmap]
rs3764311	0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs3764314	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs3812984	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs3812986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812987	0.82[JPT][hapmap]
rs3844425	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3852781	0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.89[ASN][1000 genomes]
rs3852782	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3852784	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3890860	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3909541	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3909542	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4238964	0.90[JPT][hapmap]
rs4788458	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4788461	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4788464	0.82[EUR][1000 genomes]
rs4788609	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4788610	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56139130	0.83[ASN][1000 genomes]
rs6499557	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6499562	0.95[JPT][hapmap]
rs6499563	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6499564	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6680	0.81[JPT][hapmap]
rs7184169	0.81[JPT][hapmap]
rs7185840	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7186155	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7188962	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7189115	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7189591	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7190994	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7190995	0.82[JPT][hapmap];0.84[YRI][hapmap]
rs7191127	0.82[JPT][hapmap];0.84[YRI][hapmap]
rs7192848	0.85[JPT][hapmap]
rs7194397	0.89[ASN][1000 genomes]
rs7194668	0.88[ASN][1000 genomes]
rs7197020	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7199261	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7200003	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7200854	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7201225	0.85[JPT][hapmap]
rs7201643	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7201866	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7202268	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7203426	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7203821	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8043606	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8044555	0.81[JPT][hapmap]
rs8044868	0.95[JPT][hapmap]
rs8050238	0.81[JPT][hapmap]
rs8051882	0.81[JPT][hapmap];0.86[YRI][hapmap]
rs8052338	0.91[JPT][hapmap]
rs8052408	0.95[JPT][hapmap]
rs8059437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8060770	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8062895	0.93[YRI][hapmap]
rs8182213	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9924964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9926156	0.82[JPT][hapmap];0.89[YRI][hapmap]
rs9926927	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9927526	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9928157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9930890	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9932062	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9932951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9936642	0.85[JPT][hapmap]
rs9938382	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9941087	0.81[JPT][hapmap]
rs9941346	0.81[AFR][1000 genomes];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7940	DHX38	cis	Lymphoblastoid	GTEx
rs7940	DHX38	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72129400-72147800	Strong transcription	Primary T cells from cord blood	blood
2	chr16:72129800-72146600	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr16:72129800-72147000	Strong transcription	Ovary	ovary
4	chr16:72129800-72147200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr16:72129800-72147600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr16:72129800-72147800	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr16:72129800-72148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:72129800-72149000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr16:72130000-72146600	Strong transcription	HUVEC	blood vessel
10	chr16:72130000-72146800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr16:72130000-72146800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr16:72130000-72147000	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr16:72130000-72147000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr16:72130000-72147000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr16:72130000-72147000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr16:72130000-72147000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr16:72130000-72147000	Strong transcription	Esophagus	oesophagus
18	chr16:72130000-72147000	Strong transcription	NHEK	skin
19	chr16:72130000-72147200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr16:72130000-72147200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:72130000-72147200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr16:72130000-72147200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr16:72130000-72147200	Strong transcription	Aorta	Aorta
24	chr16:72130000-72147200	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr16:72130000-72147200	Strong transcription	Brain Substantia Nigra	brain
26	chr16:72130000-72147200	Strong transcription	Fetal Lung	lung
27	chr16:72130000-72147200	Strong transcription	Left Ventricle	heart
28	chr16:72130000-72147400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr16:72130000-72147400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr16:72130000-72147400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr16:72130000-72147400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr16:72130000-72147400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:72130000-72147400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:72130000-72147400	Strong transcription	Adipose Nuclei	Adipose
35	chr16:72130000-72147400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr16:72130000-72147400	Strong transcription	Fetal Brain Female	brain
37	chr16:72130000-72147400	Strong transcription	Fetal Thymus	thymus
38	chr16:72130000-72147400	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr16:72130000-72147400	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr16:72130000-72147600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr16:72130000-72147600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr16:72130000-72147600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr16:72130000-72147600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:72130000-72147600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr16:72130000-72147600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr16:72130000-72147600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr16:72130000-72147600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr16:72130000-72147600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr16:72130000-72147600	Strong transcription	NHLF	lung
50	chr16:72130000-72147800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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