Variant report

Variant	rs297127
Chromosome Location	chr2:39298071-39298072
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	chr2:39297576..39299588-chr2:39304376..39306926,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10165968	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10169337	0.86[ASN][1000 genomes]
rs10177250	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10184015	0.86[EUR][1000 genomes]
rs10190377	0.91[EUR][1000 genomes]
rs10200058	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10205802	0.86[ASN][1000 genomes]
rs10206751	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11124660	0.81[EUR][1000 genomes]
rs11674846	0.83[ASN][1000 genomes]
rs11691035	0.83[ASN][1000 genomes]
rs12620003	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12620071	0.83[EUR][1000 genomes]
rs12622969	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13031871	0.86[EUR][1000 genomes]
rs13033392	0.91[EUR][1000 genomes]
rs1377860	0.83[EUR][1000 genomes]
rs1377861	0.83[EUR][1000 genomes]
rs1377864	0.86[EUR][1000 genomes]
rs1454219	0.81[ASN][1000 genomes]
rs1454227	0.92[EUR][1000 genomes]
rs1470914	0.89[EUR][1000 genomes]
rs2060988	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2060989	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs212322	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2123882	0.88[EUR][1000 genomes]
rs2168043	0.84[ASN][1000 genomes]
rs2373497	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2924714	0.83[EUR][1000 genomes]
rs2969763	0.83[EUR][1000 genomes]
rs297120	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs297121	0.83[EUR][1000 genomes]
rs297124	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297125	0.83[EUR][1000 genomes]
rs297128	0.83[EUR][1000 genomes]
rs297129	0.83[EUR][1000 genomes]
rs297130	0.83[EUR][1000 genomes]
rs297131	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs297132	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs297133	0.83[EUR][1000 genomes]
rs297134	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs297135	0.83[EUR][1000 genomes]
rs297136	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs297137	0.83[EUR][1000 genomes]
rs297139	0.83[EUR][1000 genomes]
rs297140	0.83[EUR][1000 genomes]
rs297141	0.83[EUR][1000 genomes]
rs297142	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs297143	0.83[EUR][1000 genomes]
rs297144	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs297145	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs297147	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs297148	0.83[EUR][1000 genomes]
rs297149	0.83[EUR][1000 genomes]
rs297150	0.83[EUR][1000 genomes]
rs297151	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs297152	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs297153	0.83[EUR][1000 genomes]
rs297155	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs297156	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs297157	0.83[EUR][1000 genomes]
rs297158	0.81[EUR][1000 genomes]
rs297159	0.83[EUR][1000 genomes]
rs297161	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297162	0.88[ASN][1000 genomes]
rs366840	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs378698	0.83[EUR][1000 genomes]
rs3796038	0.89[EUR][1000 genomes]
rs388958	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4670905	0.83[EUR][1000 genomes]
rs57378308	0.81[EUR][1000 genomes]
rs59732351	0.81[EUR][1000 genomes]
rs61405040	0.83[EUR][1000 genomes]
rs6419600	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544191	0.83[EUR][1000 genomes]
rs6544197	0.83[EUR][1000 genomes]
rs6726833	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6739807	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6758330	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72909662	0.81[EUR][1000 genomes]
rs7604229	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7607509	0.86[ASN][1000 genomes]
rs970409	0.83[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
rs297127	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 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	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
6	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
7	chr2:39236000-39305600	Weak transcription	Gastric	stomach
8	chr2:39236200-39305600	Weak transcription	Lung	lung
9	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
11	chr2:39250200-39313600	Weak transcription	Brain Angular Gyrus	brain
12	chr2:39250400-39303000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
14	chr2:39255000-39299000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:39258400-39299200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:39258400-39322400	Weak transcription	Thymus	Thymus
17	chr2:39261000-39309800	Weak transcription	Spleen	Spleen
18	chr2:39261000-39318800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:39261000-39327800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:39271400-39320400	Weak transcription	Right Ventricle	heart
21	chr2:39272800-39310200	Weak transcription	Fetal Heart	heart
22	chr2:39275200-39299000	Weak transcription	Brain Germinal Matrix	brain
23	chr2:39275200-39299000	Weak transcription	Fetal Brain Female	brain
24	chr2:39276200-39301400	Weak transcription	Fetal Intestine Small	intestine
25	chr2:39278200-39314800	Weak transcription	Left Ventricle	heart
26	chr2:39280800-39334200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:39281400-39301600	Weak transcription	Fetal Stomach	stomach
28	chr2:39282600-39327400	Weak transcription	Hela-S3	cervix
29	chr2:39283200-39299200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:39286600-39298200	Weak transcription	Right Atrium	heart
31	chr2:39288800-39298800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:39289200-39303200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:39293400-39314800	Weak transcription	Psoas Muscle	Psoas
34	chr2:39293600-39298200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:39293600-39299000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:39293600-39310200	Weak transcription	Fetal Lung	lung
37	chr2:39293600-39322000	Weak transcription	NHDF-Ad	bronchial
38	chr2:39293800-39310200	Weak transcription	Primary T cells from cord blood	blood
39	chr2:39293800-39339400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:39294000-39299000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:39294000-39299000	Weak transcription	Fetal Brain Male	brain
42	chr2:39294000-39299200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:39294000-39305400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:39294000-39307000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:39294000-39312000	Weak transcription	K562	blood
46	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
47	chr2:39294200-39303000	Weak transcription	A549	lung
48	chr2:39294200-39322000	Weak transcription	Dnd41	blood
49	chr2:39294400-39298200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:39294400-39298800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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