Variant report

Variant	rs12622969
Chromosome Location	chr2:39343183-39343184
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39332401..39334578-chr2:39342620..39345134,2	K562	blood:
2	chr2:39342942..39343638-chr9:34310057..34310557,2	MCF-7	breast:
3	chr2:39342488..39346158-chr2:39346528..39349240,5	MCF-7	breast:
4	chr2:39331060..39334578-chr2:39342620..39345134,3	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10153761	0.82[EUR][1000 genomes]
rs10165968	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10166395	1.00[CEU][hapmap]
rs10166801	0.81[EUR][1000 genomes]
rs10169337	0.80[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10172085	0.81[EUR][1000 genomes]
rs10177250	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10184015	0.89[EUR][1000 genomes]
rs10190377	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs10194374	0.81[EUR][1000 genomes]
rs10200058	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10205802	0.80[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10206751	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1037495	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs1043793	1.00[CEU][hapmap]
rs10439459	0.82[EUR][1000 genomes]
rs11124659	0.82[EUR][1000 genomes]
rs11124660	0.87[EUR][1000 genomes]
rs11692687	0.82[EUR][1000 genomes]
rs12471731	1.00[CEU][hapmap]
rs12620003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12620071	0.85[EUR][1000 genomes]
rs13031871	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs1454226	0.82[EUR][1000 genomes]
rs1454227	0.92[EUR][1000 genomes]
rs1470914	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes]
rs1470915	0.82[EUR][1000 genomes]
rs2060988	0.80[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs2060989	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs212322	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2123881	0.82[EUR][1000 genomes]
rs2123882	0.91[EUR][1000 genomes]
rs2168043	0.86[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2373474	0.81[EUR][1000 genomes]
rs2373497	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2888585	0.82[EUR][1000 genomes]
rs2924714	0.85[EUR][1000 genomes]
rs2969763	0.85[EUR][1000 genomes]
rs297120	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs297121	0.85[EUR][1000 genomes]
rs297124	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297125	0.85[EUR][1000 genomes]
rs297127	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs297128	0.85[EUR][1000 genomes]
rs297129	0.85[EUR][1000 genomes]
rs297130	0.85[EUR][1000 genomes]
rs297131	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297132	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297133	0.85[EUR][1000 genomes]
rs297134	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297135	0.85[EUR][1000 genomes]
rs297136	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297137	0.85[EUR][1000 genomes]
rs297139	0.85[EUR][1000 genomes]
rs297140	0.85[EUR][1000 genomes]
rs297141	0.85[EUR][1000 genomes]
rs297142	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297143	0.85[EUR][1000 genomes]
rs297144	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297145	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297147	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297148	0.85[EUR][1000 genomes]
rs297149	0.85[EUR][1000 genomes]
rs297150	0.85[EUR][1000 genomes]
rs297151	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297152	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297153	0.85[EUR][1000 genomes]
rs297155	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297156	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297157	0.85[EUR][1000 genomes]
rs297158	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs297159	0.85[EUR][1000 genomes]
rs297160	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs297161	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297162	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs366840	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs378698	0.85[EUR][1000 genomes]
rs3796038	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs388958	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670269	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs4670902	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
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	1.00[CEU][hapmap];0.97[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544191	0.85[EUR][1000 genomes]
rs6544197	0.85[EUR][1000 genomes]
rs6713281	0.82[EUR][1000 genomes]
rs6725356	0.81[EUR][1000 genomes]
rs6725644	0.81[EUR][1000 genomes]
rs6726833	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739807	0.83[EUR][1000 genomes]
rs6758330	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes]
rs72909662	0.87[EUR][1000 genomes]
rs7607509	0.80[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs963730	1.00[CEU][hapmap]
rs970409	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
rs12622969	SOS1	cis	multi-tissue	Pritchard
rs12622969	SOS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
2	chr2:39319800-39343200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:39321000-39344600	Weak transcription	Gastric	stomach
4	chr2:39322400-39345200	Weak transcription	Osteobl	bone
5	chr2:39322600-39344400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:39322800-39345200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:39323000-39344800	Weak transcription	Primary T cells from cord blood	blood
8	chr2:39327000-39344600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39328000-39346800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:39328200-39344600	Weak transcription	Hela-S3	cervix
11	chr2:39330000-39346800	Weak transcription	Spleen	Spleen
12	chr2:39334200-39345000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:39334600-39344400	Weak transcription	Small Intestine	intestine
14	chr2:39334600-39344600	Weak transcription	NHLF	lung
15	chr2:39334600-39345200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:39334600-39345400	Weak transcription	NH-A	brain
17	chr2:39334600-39346000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:39334600-39346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:39334800-39343200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:39334800-39345200	Weak transcription	HSMMtube	muscle
21	chr2:39334800-39345400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:39334800-39345600	Weak transcription	HSMM	muscle
23	chr2:39335000-39344800	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:39335200-39344400	Weak transcription	Liver	Liver
25	chr2:39335200-39344600	Weak transcription	Brain Anterior Caudate	brain
26	chr2:39335200-39344800	Weak transcription	Ovary	ovary
27	chr2:39335200-39345000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:39335200-39345200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:39335200-39345800	Weak transcription	Brain Substantia Nigra	brain
30	chr2:39335400-39344400	Weak transcription	Fetal Heart	heart
31	chr2:39335400-39344600	Weak transcription	NHEK	skin
32	chr2:39335400-39345000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:39335400-39345400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:39335600-39344600	Weak transcription	Fetal Brain Female	brain
35	chr2:39335600-39345200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:39335600-39345200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:39335600-39345200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:39335800-39344400	Weak transcription	K562	blood
39	chr2:39336000-39345400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:39336200-39343200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:39337000-39345200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:39337200-39344800	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:39337400-39343800	Weak transcription	Fetal Brain Male	brain
44	chr2:39337400-39345400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:39337800-39343400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:39337800-39344800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:39337800-39345200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:39338000-39345200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:39338600-39344000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:39338800-39344600	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links