Variant report

Variant	rs425964
Chromosome Location	chr7:101603996-101603997
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:101591850..101595960-chr7:101603598..101607099,3	MCF-7	breast:
2	chr7:101601045..101603669-chr7:101603996..101606594,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH2B2-7	chr7:101603396-101605174	ENSG00000272219.1

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction
ENSG00000272219	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2906649	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2906653	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2970477	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2970478	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2970493	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2970494	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs385854	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs386137	0.83[ASN][1000 genomes]
rs404284	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs414438	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs416466	0.80[ASN][1000 genomes]
rs425768	0.80[ASN][1000 genomes]
rs427039	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs433736	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs434564	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs440923	0.85[ASN][1000 genomes]
rs441601	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs441780	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729764	0.81[ASN][1000 genomes]
rs6954798	0.86[ASN][1000 genomes]
rs727544	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs740302	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs876826	0.86[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv888827	chr7:101562674-101650302	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101578200-101612000	Weak transcription	HepG2	liver
2	chr7:101578200-101671200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:101583400-101608000	Weak transcription	Primary B cells from cord blood	blood
4	chr7:101586400-101615800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:101586400-101620600	Weak transcription	Adipose Nuclei	Adipose
6	chr7:101591400-101628200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:101591600-101607800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:101592400-101629200	Weak transcription	Aorta	Aorta
9	chr7:101594800-101612400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:101596200-101606200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:101596200-101606400	Weak transcription	Thymus	Thymus
12	chr7:101596200-101615400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:101596400-101606400	Weak transcription	Pancreas	Pancrea
14	chr7:101596400-101608000	Weak transcription	Spleen	Spleen
15	chr7:101596400-101615800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:101596800-101614200	Weak transcription	K562	blood
17	chr7:101597000-101608400	Weak transcription	Small Intestine	intestine
18	chr7:101597000-101642000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:101597200-101621200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:101597400-101604200	Weak transcription	Liver	Liver
21	chr7:101597400-101608000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:101597400-101616400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:101597400-101624800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:101597400-101625400	Weak transcription	NHLF	lung
25	chr7:101597600-101615800	Weak transcription	Primary T cells from cord blood	blood
26	chr7:101597600-101624600	Weak transcription	Hela-S3	cervix
27	chr7:101598000-101608600	Weak transcription	Ovary	ovary
28	chr7:101598200-101631600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:101598400-101606400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:101598600-101606400	Weak transcription	Lung	lung
31	chr7:101598600-101608000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:101598600-101612800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:101598800-101604200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr7:101598800-101608000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr7:101598800-101615800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr7:101599000-101607800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:101599000-101612800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:101599200-101626200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr7:101600200-101604200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr7:101600800-101608200	Weak transcription	Right Atrium	heart
41	chr7:101601200-101604400	Strong transcription	Fetal Intestine Small	intestine
42	chr7:101601600-101606800	Weak transcription	Fetal Thymus	thymus
43	chr7:101601600-101607800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr7:101601600-101626600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr7:101601800-101604000	Weak transcription	Right Ventricle	heart
46	chr7:101601800-101604400	Weak transcription	Fetal Stomach	stomach
47	chr7:101601800-101607000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr7:101601800-101607800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:101601800-101613600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:101601800-101615600	Weak transcription	Fetal Muscle Leg	muscle

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