Variant report

Variant	rs297143
Chromosome Location	chr2:39320067-39320068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39318488..39322195-chr2:39323167..39328240,4	K562	blood:
2	chr2:39319265..39325749-chr2:39345590..39349573,11	MCF-7	breast:
3	chr2:39319231..39321198-chr2:39347034..39349662,2	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction
ENSG00000225900	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10153761	0.96[EUR][1000 genomes]
rs10165968	0.87[EUR][1000 genomes]
rs10166801	0.94[EUR][1000 genomes]
rs10172085	0.91[EUR][1000 genomes]
rs10177250	0.83[EUR][1000 genomes]
rs10190377	0.82[EUR][1000 genomes]
rs10194374	0.94[EUR][1000 genomes]
rs10200058	0.82[EUR][1000 genomes]
rs10439459	0.96[EUR][1000 genomes]
rs11124659	0.96[EUR][1000 genomes]
rs11124660	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11692687	0.96[EUR][1000 genomes]
rs12620003	0.87[EUR][1000 genomes]
rs12620071	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12622969	0.85[EUR][1000 genomes]
rs12712630	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13033392	0.82[EUR][1000 genomes]
rs1377860	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1377861	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1377863	0.93[EUR][1000 genomes]
rs1454220	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1454226	0.96[EUR][1000 genomes]
rs1454227	0.84[EUR][1000 genomes]
rs1454228	0.91[EUR][1000 genomes]
rs1470914	0.80[EUR][1000 genomes]
rs1470915	0.96[EUR][1000 genomes]
rs1840281	0.91[EUR][1000 genomes]
rs2060987	0.83[ASN][1000 genomes]
rs2060989	1.00[EUR][1000 genomes]
rs2123876	0.93[EUR][1000 genomes]
rs2123879	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2123881	0.96[EUR][1000 genomes]
rs2168042	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2373474	0.94[EUR][1000 genomes]
rs2373495	0.93[EUR][1000 genomes]
rs2373496	0.93[EUR][1000 genomes]
rs2888585	0.96[EUR][1000 genomes]
rs2924710	0.82[ASN][1000 genomes]
rs2924714	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2969763	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs297120	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs297121	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297122	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs297124	0.83[EUR][1000 genomes]
rs297125	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297127	0.83[EUR][1000 genomes]
rs297128	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs297129	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297130	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297131	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297132	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297133	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297134	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297135	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297136	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297137	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297139	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297140	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297141	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297142	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297144	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297145	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297147	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297149	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs297150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs297151	0.87[EUR][1000 genomes]
rs297152	0.87[EUR][1000 genomes]
rs297153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs297155	0.80[EUR][1000 genomes]
rs297156	0.87[EUR][1000 genomes]
rs297157	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs297158	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs297159	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297160	0.80[ASN][1000 genomes]
rs297161	0.83[EUR][1000 genomes]
rs366840	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs378698	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796038	0.80[EUR][1000 genomes]
rs388958	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs451964	0.88[ASN][1000 genomes]
rs4670272	0.93[EUR][1000 genomes]
rs4670905	1.00[EUR][1000 genomes]
rs57378308	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58645871	0.93[EUR][1000 genomes]
rs59732351	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61405040	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6419600	0.85[EUR][1000 genomes]
rs6544191	1.00[EUR][1000 genomes]
rs6544194	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6544195	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6544197	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713281	0.96[EUR][1000 genomes]
rs6725356	0.94[EUR][1000 genomes]
rs6725644	0.94[EUR][1000 genomes]
rs6726833	0.82[EUR][1000 genomes]
rs6739568	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6756184	0.93[EUR][1000 genomes]
rs72909662	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7568552	0.91[EUR][1000 genomes]
rs9309031	0.91[EUR][1000 genomes]
rs970409	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997344	0.83[EUR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs297143	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
2	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
3	chr2:39258400-39322400	Weak transcription	Thymus	Thymus
4	chr2:39261000-39327800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:39271400-39320400	Weak transcription	Right Ventricle	heart
6	chr2:39280800-39334200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:39282600-39327400	Weak transcription	Hela-S3	cervix
8	chr2:39293600-39322000	Weak transcription	NHDF-Ad	bronchial
9	chr2:39293800-39339400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
11	chr2:39294200-39322000	Weak transcription	Dnd41	blood
12	chr2:39294400-39322000	Weak transcription	HSMM	muscle
13	chr2:39294600-39320600	Weak transcription	Primary B cells from cord blood	blood
14	chr2:39294600-39320800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:39294600-39339400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:39294800-39320400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:39294800-39322000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr2:39296400-39320600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:39296400-39322600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:39296400-39339400	Weak transcription	Aorta	Aorta
21	chr2:39296600-39322200	Weak transcription	NHEK	skin
22	chr2:39297200-39320600	Weak transcription	Adipose Nuclei	Adipose
23	chr2:39297200-39322000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:39297400-39324600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:39299600-39320600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:39301200-39322200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:39305800-39322000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:39307600-39320600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:39307600-39324600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:39307600-39333800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:39308200-39320400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:39308400-39320400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:39308600-39320800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr2:39308600-39321800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:39311000-39320600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:39311000-39322000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:39311200-39322000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:39311600-39322000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:39313600-39320800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:39313600-39322000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:39313800-39320400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:39314000-39320600	Weak transcription	Gastric	stomach
43	chr2:39314000-39322000	Weak transcription	Ovary	ovary
44	chr2:39315200-39320600	Weak transcription	Left Ventricle	heart
45	chr2:39315200-39326800	Weak transcription	Psoas Muscle	Psoas
46	chr2:39316000-39320400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:39316400-39320600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:39316600-39322000	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:39316600-39324800	Weak transcription	Placenta	Placenta
50	chr2:39318200-39320600	Weak transcription	H9 Cell Line	embryonic stem cell

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