Variant report

Variant	rs6544220
Chromosome Location	chr2:39527409-39527410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39524953..39527718-chr4:1713296..1715250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270195	Chromatin interaction
ENSG00000163950	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10153665	0.95[EUR][1000 genomes]
rs10170424	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10170617	0.80[EUR][1000 genomes]
rs10172736	0.87[EUR][1000 genomes]
rs10173556	0.87[EUR][1000 genomes]
rs10175038	0.87[EUR][1000 genomes]
rs10195629	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1035232	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10865149	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10865150	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10865152	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11124668	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11124673	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124676	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124677	0.85[ASN][1000 genomes]
rs11124679	0.82[EUR][1000 genomes]
rs1125839	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1211996	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12622941	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1468902	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17023837	0.82[EUR][1000 genomes]
rs1861735	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1922827	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2005892	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2111382	0.81[AFR][1000 genomes]
rs2178760	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2178762	0.82[EUR][1000 genomes]
rs2193422	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2373534	0.82[EUR][1000 genomes]
rs2373535	0.82[EUR][1000 genomes]
rs2542008	0.84[EUR][1000 genomes]
rs2888594	0.82[EUR][1000 genomes]
rs2888598	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3755177	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3755178	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770670	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3770675	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3770678	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6544213	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544222	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544224	0.80[EUR][1000 genomes]
rs6712274	0.82[EUR][1000 genomes]
rs6712921	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6718134	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6725938	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6732611	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6736700	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6741019	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6742170	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6743041	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6753323	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6756183	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6760382	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7574250	0.83[ASN][1000 genomes]
rs7578136	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7579414	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs759589	0.89[EUR][1000 genomes]
rs7600014	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7600046	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7601700	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7603337	0.85[EUR][1000 genomes]
rs7604047	0.81[EUR][1000 genomes]
rs7608153	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv873886	chr2:39468676-39573521	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	esv1809158	chr2:39474679-39588797	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	esv1828851	chr2:39508121-39588797	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv873888	chr2:39508830-39573521	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544220	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39478600-39543400	Weak transcription	Stomach Mucosa	stomach
3	chr2:39481000-39580200	Weak transcription	NHEK	skin
4	chr2:39493600-39565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:39494000-39553000	Weak transcription	GM12878-XiMat	blood
6	chr2:39504600-39540000	Weak transcription	Right Ventricle	heart
7	chr2:39504600-39562000	Weak transcription	Psoas Muscle	Psoas
8	chr2:39504800-39527800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:39504800-39538400	Weak transcription	Small Intestine	intestine
10	chr2:39504800-39541600	Weak transcription	Fetal Brain Male	brain
11	chr2:39504800-39565800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:39504800-39567200	Weak transcription	Hela-S3	cervix
13	chr2:39505000-39538200	Weak transcription	Lung	lung
14	chr2:39505400-39556800	Weak transcription	Thymus	Thymus
15	chr2:39505400-39557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:39505400-39562400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:39505600-39540000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:39507200-39538400	Weak transcription	Aorta	Aorta
19	chr2:39513600-39555000	Weak transcription	Primary B cells from cord blood	blood
20	chr2:39514400-39539800	Weak transcription	A549	lung
21	chr2:39514400-39541800	Weak transcription	HUVEC	blood vessel
22	chr2:39515200-39538600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:39516200-39557600	Weak transcription	Gastric	stomach
24	chr2:39517200-39552400	Weak transcription	HMEC	breast
25	chr2:39517600-39566400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:39519000-39531600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:39519000-39531800	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:39519000-39538600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:39519000-39555200	Weak transcription	Fetal Thymus	thymus
30	chr2:39519800-39527800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:39519800-39538400	Weak transcription	Brain Anterior Caudate	brain
32	chr2:39519800-39538400	Weak transcription	Esophagus	oesophagus
33	chr2:39519800-39553000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:39519800-39555400	Weak transcription	Fetal Heart	heart
35	chr2:39519800-39562200	Weak transcription	K562	blood
36	chr2:39519800-39583000	Weak transcription	Brain Angular Gyrus	brain
37	chr2:39520000-39537200	Weak transcription	NH-A	brain
38	chr2:39520000-39538800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr2:39520000-39539400	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:39520000-39556600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:39520000-39586200	Weak transcription	Fetal Kidney	kidney
42	chr2:39520200-39527800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:39520200-39538200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:39520200-39539800	Weak transcription	Fetal Brain Female	brain
45	chr2:39520200-39553200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:39520200-39555200	Weak transcription	Ovary	ovary
47	chr2:39520400-39536400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:39520400-39538200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:39520400-39538200	Weak transcription	Fetal Intestine Small	intestine
50	chr2:39520400-39538200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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