Variant report

Variant	rs58414903
Chromosome Location	chr7:101688121-101688122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:60639525..60641886-chr7:101687189..101690169,2	MCF-7	breast:
2	chr20:60640086..60642079-chr7:101687169..101688689,3	MCF-7	breast:
3	chr7:101688104..101690930-chr7:101693641..101697108,3	MCF-7	breast:
4	chr20:60640319..60642125-chr7:101687169..101688689,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH2B2-5	chr7:101685040-101688225	ucscGeneNc_uc003uyy_2

Variant related genes	Relation type
ENSG00000130699	Chromatin interaction
ENSG00000265306	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10231704	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10245459	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10245816	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246310	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249739	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252737	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261132	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975663	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979916	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11982462	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537930	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538702	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539349	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540846	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17410356	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17495148	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17495210	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28401723	0.88[EUR][1000 genomes]
rs28502241	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715744	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55704423	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55851631	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55974420	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67245174	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67737740	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959827	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73185880	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185883	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185884	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9655773	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv482521	chr7:101604002-101718950	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv831080	chr7:101629121-101718950	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1027574	chr7:101654060-101718950	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv607985	chr7:101683563-101718950	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101642800-101697600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:101652800-101688400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:101653000-101688200	Weak transcription	Colonic Mucosa	Colon
4	chr7:101656000-101689200	Weak transcription	Aorta	Aorta
5	chr7:101667200-101688200	Weak transcription	Brain Substantia Nigra	brain
6	chr7:101667600-101688200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:101667600-101688400	Weak transcription	Fetal Brain Female	brain
8	chr7:101668000-101707200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:101668600-101694200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:101671800-101688400	Weak transcription	Fetal Brain Male	brain
11	chr7:101672200-101692200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:101672200-101697000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:101672400-101694000	Weak transcription	Primary T cells from cord blood	blood
14	chr7:101672400-101697200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:101673000-101688200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:101673000-101689200	Weak transcription	Spleen	Spleen
17	chr7:101673200-101688200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr7:101673200-101689200	Weak transcription	Pancreas	Pancrea
19	chr7:101673200-101692800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:101673200-101694200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:101674200-101707400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:101674400-101688200	Weak transcription	Lung	lung
23	chr7:101674400-101696800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:101674400-101697000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:101674800-101692600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:101679000-101695200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:101683400-101691400	Enhancers	GM12878-XiMat	blood
28	chr7:101683600-101688200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr7:101683600-101689600	Weak transcription	Placenta	Placenta
30	chr7:101684000-101692200	Weak transcription	Fetal Intestine Large	intestine
31	chr7:101684200-101697400	Weak transcription	Liver	Liver
32	chr7:101685600-101688200	Weak transcription	HSMMtube	muscle
33	chr7:101685600-101697200	Weak transcription	HepG2	liver
34	chr7:101685800-101688200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:101685800-101688200	Weak transcription	Stomach Mucosa	stomach
36	chr7:101685800-101694000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr7:101685800-101694000	Weak transcription	NHEK	skin
38	chr7:101686000-101691000	Weak transcription	A549	lung
39	chr7:101686400-101688200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:101686400-101694000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:101686800-101688200	Strong transcription	Fetal Intestine Small	intestine
42	chr7:101686800-101693800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr7:101687400-101688200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:101687800-101688200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:101687800-101688200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:101687800-101688200	Enhancers	Dnd41	blood
47	chr7:101687800-101688200	Enhancers	NHLF	lung
48	chr7:101687800-101688400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr7:101687800-101688400	Enhancers	NH-A	brain
50	chr7:101687800-101689800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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