Variant report

Variant	rs297147
Chromosome Location	chr2:39322942-39322943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39319265..39325749-chr2:39345590..39349573,11	MCF-7	breast:
2	chr2:39321313..39323497-chr2:39324188..39326712,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction
ENSG00000225900	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10153761	0.82[EUR][1000 genomes]
rs10165968	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10166801	0.81[EUR][1000 genomes]
rs10169337	0.86[ASN][1000 genomes]
rs10172085	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10177250	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10184015	0.89[EUR][1000 genomes]
rs10190377	0.94[EUR][1000 genomes]
rs10194374	0.81[EUR][1000 genomes]
rs10200058	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10205802	0.86[ASN][1000 genomes]
rs10206751	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10439459	0.82[EUR][1000 genomes]
rs11124659	0.82[EUR][1000 genomes]
rs11124660	0.87[EUR][1000 genomes]
rs11674846	0.85[ASN][1000 genomes]
rs11691035	0.85[ASN][1000 genomes]
rs11692687	0.82[EUR][1000 genomes]
rs12620003	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12620071	0.85[EUR][1000 genomes]
rs12622969	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13031871	0.89[EUR][1000 genomes]
rs13033392	0.94[EUR][1000 genomes]
rs1377860	0.85[EUR][1000 genomes]
rs1377861	0.85[EUR][1000 genomes]
rs1377863	0.82[EUR][1000 genomes]
rs1377864	0.89[EUR][1000 genomes]
rs1454219	0.83[ASN][1000 genomes]
rs1454226	0.82[EUR][1000 genomes]
rs1454227	0.92[EUR][1000 genomes]
rs1470914	0.92[EUR][1000 genomes]
rs1470915	0.82[EUR][1000 genomes]
rs2060988	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2060989	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212322	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2123881	0.82[EUR][1000 genomes]
rs2123882	0.91[EUR][1000 genomes]
rs2168043	0.86[ASN][1000 genomes]
rs2373474	0.81[EUR][1000 genomes]
rs2373497	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2888585	0.82[EUR][1000 genomes]
rs2924714	0.85[EUR][1000 genomes]
rs2969763	0.85[EUR][1000 genomes]
rs297120	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs297121	0.85[EUR][1000 genomes]
rs297124	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs297125	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297127	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs297128	0.85[EUR][1000 genomes]
rs297129	0.85[EUR][1000 genomes]
rs297130	0.85[EUR][1000 genomes]
rs297131	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297132	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297133	0.85[EUR][1000 genomes]
rs297134	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297135	0.85[EUR][1000 genomes]
rs297136	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297137	0.85[EUR][1000 genomes]
rs297139	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297140	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297141	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297142	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297143	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297144	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297145	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297148	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297149	0.85[EUR][1000 genomes]
rs297150	0.85[EUR][1000 genomes]
rs297151	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs297152	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs297153	0.85[EUR][1000 genomes]
rs297155	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs297156	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs297157	0.85[EUR][1000 genomes]
rs297158	0.87[EUR][1000 genomes]
rs297159	0.85[EUR][1000 genomes]
rs297161	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs297162	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs366840	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs378698	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3796038	0.92[EUR][1000 genomes]
rs388958	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4670905	0.85[EUR][1000 genomes]
rs57378308	0.87[EUR][1000 genomes]
rs59732351	0.87[EUR][1000 genomes]
rs61405040	0.85[EUR][1000 genomes]
rs6419600	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6544191	0.85[EUR][1000 genomes]
rs6544197	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6713281	0.82[EUR][1000 genomes]
rs6725356	0.81[EUR][1000 genomes]
rs6725644	0.81[EUR][1000 genomes]
rs6726833	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6739807	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6758330	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72909662	0.87[EUR][1000 genomes]
rs7604229	0.86[ASN][1000 genomes]
rs7607509	0.86[ASN][1000 genomes]
rs970409	0.85[EUR][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
rs297147	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 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	chr2:39261000-39327800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:39280800-39334200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:39282600-39327400	Weak transcription	Hela-S3	cervix
6	chr2:39293800-39339400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
8	chr2:39294600-39339400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:39296400-39339400	Weak transcription	Aorta	Aorta
10	chr2:39297400-39324600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:39307600-39324600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:39307600-39333800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:39315200-39326800	Weak transcription	Psoas Muscle	Psoas
14	chr2:39316600-39324800	Weak transcription	Placenta	Placenta
15	chr2:39319000-39333800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:39319600-39327800	Weak transcription	Lung	lung
17	chr2:39319600-39328200	Weak transcription	Right Atrium	heart
18	chr2:39319600-39339600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:39319800-39333800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:39319800-39343200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:39320600-39323200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:39320600-39323200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:39320600-39323400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:39320600-39323600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr2:39321000-39324400	Weak transcription	Right Ventricle	heart
26	chr2:39321000-39326400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:39321000-39326800	Weak transcription	Left Ventricle	heart
28	chr2:39321000-39327600	Weak transcription	Stomach Mucosa	stomach
29	chr2:39321000-39334200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:39321000-39334200	Weak transcription	Liver	Liver
31	chr2:39321000-39338600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:39321000-39344600	Weak transcription	Gastric	stomach
33	chr2:39321200-39324800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:39321200-39331000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:39321200-39333800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:39321600-39324600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:39321600-39326800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:39321800-39323200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:39321800-39323200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:39321800-39323200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:39321800-39323400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr2:39321800-39324600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:39321800-39332400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:39322000-39323000	Enhancers	Primary hematopoietic stem cells	blood
45	chr2:39322000-39323000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:39322000-39323000	Enhancers	Fetal Lung	lung
47	chr2:39322000-39323000	Enhancers	Fetal Stomach	stomach
48	chr2:39322000-39323000	Enhancers	NHDF-Ad	bronchial
49	chr2:39322000-39323200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:39322000-39323200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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