Variant report

Variant	rs10941359
Chromosome Location	chr5:37670562-37670563
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37667989..37670619-chr5:37702239..37705026,2	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10062316	0.81[CHB][hapmap]
rs1013398	0.81[CHB][hapmap]
rs10805627	0.94[ASN][1000 genomes]
rs10941344	0.81[CHB][hapmap]
rs10941345	0.82[CHB][hapmap]
rs10941347	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs10941348	0.82[CHB][hapmap]
rs10941351	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs10941352	0.81[CHB][hapmap]
rs10941353	0.82[CHB][hapmap]
rs10941356	0.82[CHB][hapmap]
rs10941358	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1126290	0.86[AMR][1000 genomes]
rs11739400	0.99[ASN][1000 genomes]
rs11740897	0.97[ASN][1000 genomes]
rs11742904	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11745980	0.99[ASN][1000 genomes]
rs11747548	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11747900	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11749563	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11750837	0.95[ASN][1000 genomes]
rs11750840	0.95[ASN][1000 genomes]
rs11949124	0.82[CHB][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs11950295	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs11954727	0.81[CHB][hapmap]
rs11957813	0.82[CHB][hapmap]
rs12152831	0.82[CHB][hapmap]
rs12189078	0.91[ASN][1000 genomes]
rs12332088	0.98[ASN][1000 genomes]
rs12516955	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12520944	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs12521063	0.90[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12654893	0.82[CHB][hapmap]
rs12655908	0.82[CHB][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes]
rs1356433	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs1400851	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs1400854	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1517785	0.82[CHB][hapmap]
rs1517786	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs1589116	0.81[CEU][hapmap];0.81[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1589119	0.94[ASN][1000 genomes]
rs1996427	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2088077	0.82[CHB][hapmap]
rs2101786	0.82[CHB][hapmap]
rs2176478	0.89[AMR][1000 genomes]
rs2176479	0.94[ASN][1000 genomes]
rs4242251	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4257799	0.87[ASN][1000 genomes]
rs4343860	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4357062	0.82[CHB][hapmap]
rs4371784	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs4451075	0.91[ASN][1000 genomes]
rs4482927	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4516881	0.96[ASN][1000 genomes]
rs4516882	0.95[ASN][1000 genomes]
rs4541680	0.92[ASN][1000 genomes]
rs4582305	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs4594879	0.91[ASN][1000 genomes]
rs4608942	0.90[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.95[ASN][1000 genomes]
rs4618454	0.94[ASN][1000 genomes]
rs4869438	0.82[CHB][hapmap]
rs4869439	0.82[CHB][hapmap]
rs4869440	0.82[CHB][hapmap];0.86[AMR][1000 genomes]
rs4869530	0.82[CHB][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes]
rs4869535	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs4869538	0.82[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4869541	0.99[ASN][1000 genomes]
rs4869543	0.94[ASN][1000 genomes]
rs55708822	0.95[ASN][1000 genomes]
rs55732996	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs55742744	0.96[ASN][1000 genomes]
rs55849485	0.87[ASN][1000 genomes]
rs55960353	0.85[AMR][1000 genomes]
rs56007806	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs56051431	0.95[ASN][1000 genomes]
rs56051756	0.95[ASN][1000 genomes]
rs56100322	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56288111	0.88[AMR][1000 genomes]
rs56412589	0.94[ASN][1000 genomes]
rs56832651	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57015453	0.87[AMR][1000 genomes]
rs59378089	0.93[ASN][1000 genomes]
rs59409868	0.97[ASN][1000 genomes]
rs59829323	0.95[ASN][1000 genomes]
rs60589722	0.94[ASN][1000 genomes]
rs61435914	0.87[AMR][1000 genomes]
rs61492379	0.91[ASN][1000 genomes]
rs62359058	0.87[AMR][1000 genomes]
rs62360907	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62360910	0.95[ASN][1000 genomes]
rs6451329	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs6451330	0.94[ASN][1000 genomes]
rs6451331	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6451333	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs6451337	0.95[ASN][1000 genomes]
rs6451339	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs6863936	1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs6864924	0.87[ASN][1000 genomes]
rs6868428	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs6874891	0.82[CHB][hapmap]
rs6884551	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs6884569	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs6885057	1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs6885329	0.94[ASN][1000 genomes]
rs6887215	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6887613	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs6889616	0.81[CHB][hapmap]
rs72743184	0.88[ASN][1000 genomes]
rs7702644	0.94[ASN][1000 genomes]
rs7703775	0.87[ASN][1000 genomes]
rs7713017	0.82[CHB][hapmap]
rs7718557	0.81[CHB][hapmap]
rs7725465	0.99[ASN][1000 genomes]
rs9292656	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv880890	chr5:37443079-37681646	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10941359	CAPSL	cis	cerebellum	SCAN
rs10941359	GDNF	cis	cerebellum	SCAN
rs10941359	WDR70	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37654600-37671800	Weak transcription	Primary T cells from cord blood	blood
2	chr5:37656600-37671600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:37662800-37671800	Weak transcription	Small Intestine	intestine
4	chr5:37664000-37671800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:37665800-37671200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:37665800-37672400	Weak transcription	Primary B cells from cord blood	blood
7	chr5:37666200-37671800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:37666200-37672200	Weak transcription	Right Ventricle	heart
9	chr5:37666400-37672400	Weak transcription	Left Ventricle	heart
10	chr5:37666600-37671800	Weak transcription	Fetal Heart	heart
11	chr5:37666800-37671400	Weak transcription	Psoas Muscle	Psoas
12	chr5:37666800-37672400	Weak transcription	Adipose Nuclei	Adipose
13	chr5:37667000-37671000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:37667000-37672200	Weak transcription	Lung	lung
15	chr5:37667400-37671800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:37668800-37671400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:37669000-37671800	Weak transcription	Ovary	ovary
18	chr5:37669200-37671000	Weak transcription	A549	lung
19	chr5:37669200-37671800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:37669200-37671800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:37669200-37671800	Weak transcription	K562	blood
22	chr5:37669200-37672400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:37669200-37672800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:37669600-37680000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:37669800-37672000	Weak transcription	NH-A	brain
26	chr5:37669800-37672200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:37669800-37672200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:37669800-37672800	Weak transcription	NHDF-Ad	bronchial
29	chr5:37670400-37670600	Enhancers	Skeletal Muscle Female	skeletal muscle

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