Variant report

Variant	rs7609455
Chromosome Location	chr2:39294787-39294788
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	chr2:39286318..39288442-chr2:39293072..39295316,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10495883	1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes]
rs17023241	0.82[JPT][hapmap]
rs17023272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2373466	1.00[GIH][hapmap]
rs2373497	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs41280639	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs55649188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57362484	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57866617	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs59340802	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59988245	0.92[AFR][1000 genomes]
rs61049772	0.93[AFR][1000 genomes]
rs61392383	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs61456571	0.95[ASN][1000 genomes]
rs61521176	0.81[ASN][1000 genomes]
rs6709646	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6722478	1.00[GIH][hapmap]
rs6729359	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6735371	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6755453	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906433	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906442	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906449	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906454	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906466	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906469	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906483	1.00[ASN][1000 genomes]
rs72909647	0.95[ASN][1000 genomes]
rs72909679	0.90[ASN][1000 genomes]
rs72918721	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7559174	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs7565814	0.82[JPT][hapmap]
rs7571797	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7581411	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7583010	0.82[JPT][hapmap]
rs7588123	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7592176	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7599990	0.82[JPT][hapmap]
rs7605889	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7609455	SOS1	cis	lymphoblastoid	seeQTL
rs7609455	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
2	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
3	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:39235600-39295800	Weak transcription	NHLF	lung
6	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
7	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
8	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
9	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:39236000-39305600	Weak transcription	Gastric	stomach
11	chr2:39236200-39305600	Weak transcription	Lung	lung
12	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
14	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:39250200-39295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:39250200-39313600	Weak transcription	Brain Angular Gyrus	brain
17	chr2:39250400-39295600	Weak transcription	NH-A	brain
18	chr2:39250400-39303000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
20	chr2:39255000-39299000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:39258400-39295800	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:39258400-39299200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:39258400-39322400	Weak transcription	Thymus	Thymus
24	chr2:39260200-39295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:39261000-39309800	Weak transcription	Spleen	Spleen
26	chr2:39261000-39318800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:39261000-39327800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:39271400-39320400	Weak transcription	Right Ventricle	heart
29	chr2:39272800-39310200	Weak transcription	Fetal Heart	heart
30	chr2:39275200-39299000	Weak transcription	Brain Germinal Matrix	brain
31	chr2:39275200-39299000	Weak transcription	Fetal Brain Female	brain
32	chr2:39276200-39301400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:39278200-39314800	Weak transcription	Left Ventricle	heart
34	chr2:39278600-39295800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:39280800-39334200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:39281400-39301600	Weak transcription	Fetal Stomach	stomach
37	chr2:39281600-39295000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:39282600-39327400	Weak transcription	Hela-S3	cervix
39	chr2:39283200-39296000	Weak transcription	Brain Anterior Caudate	brain
40	chr2:39283200-39299200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:39283400-39295400	Weak transcription	Osteobl	bone
42	chr2:39284200-39296000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:39286600-39298200	Weak transcription	Right Atrium	heart
44	chr2:39288800-39298800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:39289200-39303200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:39290400-39295400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:39291200-39296200	Strong transcription	HepG2	liver
48	chr2:39291400-39294800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:39292400-39294800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:39292400-39294800	Strong transcription	Rectal Mucosa Donor 29	rectum

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