Variant report

Variant	rs340642
Chromosome Location	chr4:87949413-87949414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87924739..87931529-chr4:87944789..87955863,16	K562	blood:
2	chr4:87855405..87858251-chr4:87947004..87950108,3	K562	blood:
3	chr4:87944509..87947205-chr4:87948010..87950101,2	K562	blood:
4	chr4:87855430..87859926-chr4:87946655..87949706,6	MCF-7	breast:
5	chr4:87947975..87950419-chr4:87957844..87960013,2	K562	blood:
6	chr4:87934960..87936958-chr4:87949259..87951055,2	MCF-7	breast:
7	chr4:87944954..87950016-chr4:87950159..87955839,10	K562	blood:
8	chr4:87926004..87930134-chr4:87942000..87950091,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10015639	0.92[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10032244	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10516788	0.90[CEU][hapmap]
rs11729622	0.89[ASN][1000 genomes]
rs13126334	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13127250	0.90[ASN][1000 genomes]
rs17012234	0.90[CEU][hapmap]
rs17701999	0.90[CEU][hapmap]
rs17752307	0.91[CEU][hapmap]
rs2007132	0.95[ASN][1000 genomes]
rs2053769	0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2053770	0.92[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs340626	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340630	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340633	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340636	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs340637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340639	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs340641	0.96[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs340643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs340648	0.94[ASN][1000 genomes]
rs340650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340651	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs375795	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs388401	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4386567	0.81[ASN][1000 genomes]
rs443459	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4693798	0.92[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4693800	0.90[ASN][1000 genomes]
rs58633957	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531941	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6531946	0.91[ASN][1000 genomes]
rs6531948	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6811587	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819155	0.90[CEU][hapmap]
rs6839933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6840258	0.90[CEU][hapmap]
rs6854749	0.91[CEU][hapmap]
rs7657530	0.82[CHB][hapmap]
rs7665282	0.91[CEU][hapmap]
rs767315	0.85[CEU][hapmap]
rs7682652	0.91[CEU][hapmap]
rs867196	0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9715807	0.90[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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87930600-87950000	Weak transcription	Fetal Stomach	stomach
2	chr4:87935600-87950200	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:87935800-87951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:87936000-87950000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:87937000-87950400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:87937000-87951800	Weak transcription	NHEK	skin
7	chr4:87937000-87952000	Weak transcription	HMEC	breast
8	chr4:87937600-87949800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:87939400-87950800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87939600-87950000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:87939600-87950400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:87940600-87950600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:87942600-87950400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:87943200-87951400	Weak transcription	Fetal Brain Male	brain
15	chr4:87944200-87951800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr4:87944200-87951800	Enhancers	K562	blood
17	chr4:87944200-87953000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:87944200-87960800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:87944800-87961600	Enhancers	Fetal Heart	heart
20	chr4:87945000-87951800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:87945400-87950000	Weak transcription	Aorta	Aorta
22	chr4:87945400-87951200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:87945600-87952000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:87946400-87951000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:87946600-87950400	Weak transcription	NHDF-Ad	bronchial
26	chr4:87946600-87951600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:87946600-87951600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:87946600-87952000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr4:87946800-87949800	Enhancers	Primary hematopoietic stem cells	blood
30	chr4:87946800-87950000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:87946800-87950600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:87947000-87949800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:87947000-87950400	Weak transcription	NHLF	lung
34	chr4:87947000-87950600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:87947000-87952000	Enhancers	Rectal Smooth Muscle	rectum
36	chr4:87947200-87952000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:87947200-87952000	Weak transcription	Gastric	stomach
38	chr4:87947800-87950000	Weak transcription	Placenta	Placenta
39	chr4:87947800-87950200	Weak transcription	Brain Substantia Nigra	brain
40	chr4:87947800-87951000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr4:87947800-87951400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:87947800-87951400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:87947800-87951800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr4:87947800-87951800	Enhancers	Colon Smooth Muscle	Colon
45	chr4:87947800-87951800	Weak transcription	Esophagus	oesophagus
46	chr4:87947800-87952000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:87947800-87952000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:87947800-87952000	Weak transcription	Lung	lung
49	chr4:87947800-87957200	Weak transcription	Dnd41	blood
50	chr4:87948000-87950000	Weak transcription	Duodenum Mucosa	Duodenum

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