Variant report

Variant	rs2983348
Chromosome Location	chr10:52279502-52279503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52272246..52274913-chr10:52277739..52279580,2	MCF-7	breast:
2	chr10:52176158..52178831-chr10:52279498..52281000,2	MCF-7	breast:
3	chr10:52269188..52271460-chr10:52277484..52280153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1203374	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203379	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203380	0.83[TSI][hapmap]
rs1203383	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203384	0.91[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203391	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203402	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203412	0.91[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203416	1.00[ASN][1000 genomes]
rs1203417	1.00[ASN][1000 genomes]
rs1203419	1.00[ASN][1000 genomes]
rs1203422	1.00[ASN][1000 genomes]
rs1203426	0.85[EUR][1000 genomes]
rs1203427	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209146	0.85[EUR][1000 genomes]
rs1211373	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1212555	0.89[TSI][hapmap]
rs2024871	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064760	0.85[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2208035	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208037	0.93[YRI][hapmap]
rs2339508	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2339509	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2474611	1.00[ASN][1000 genomes]
rs2574945	1.00[ASN][1000 genomes]
rs2574976	0.93[GIH][hapmap];1.00[ASN][1000 genomes]
rs2688874	1.00[ASN][1000 genomes]
rs2688876	1.00[ASN][1000 genomes]
rs2688883	1.00[ASN][1000 genomes]
rs2688884	0.93[GIH][hapmap];1.00[ASN][1000 genomes]
rs2842099	1.00[ASN][1000 genomes]
rs2842110	1.00[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs2860490	1.00[ASW][hapmap];0.87[LWK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs2983346	0.94[EUR][1000 genomes]
rs2983349	0.94[EUR][1000 genomes]
rs2983352	1.00[ASW][hapmap];0.87[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2983358	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2983362	1.00[ASW][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs2983363	1.00[ASW][hapmap];0.87[LWK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs2983372	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	1.00[ASW][hapmap];0.87[LWK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs3011712	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011715	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011778	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3011781	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3011795	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011799	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7078586	0.86[TSI][hapmap]
rs7094723	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs72801753	1.00[ASN][1000 genomes]
rs7923756	1.00[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs910818	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs910819	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9416590	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv895392	chr10:52263910-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv467193	chr10:52265265-52289664	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv550855	chr10:52265265-52289664	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2983348	CSTF2T	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:52266800-52282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:52267000-52282400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr10:52268200-52282400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr10:52268200-52282600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:52268400-52282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr10:52270000-52282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:52270000-52282800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr10:52270200-52282600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:52271200-52283000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:52271600-52300600	Weak transcription	Aorta	Aorta
12	chr10:52271800-52280800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr10:52272200-52281000	Weak transcription	Fetal Intestine Large	intestine
14	chr10:52272400-52280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr10:52272400-52280400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr10:52272400-52284600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
18	chr10:52272800-52281200	Weak transcription	Ovary	ovary
19	chr10:52272800-52281400	Weak transcription	Placenta	Placenta
20	chr10:52272800-52281600	Weak transcription	HepG2	liver
21	chr10:52272800-52288200	Weak transcription	HSMMtube	muscle
22	chr10:52273200-52281000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr10:52273200-52281600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:52273200-52282600	Weak transcription	Right Ventricle	heart
25	chr10:52273200-52285800	Weak transcription	K562	blood
26	chr10:52273200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:52273200-52287400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr10:52273200-52288400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr10:52273400-52281000	Weak transcription	Fetal Muscle Leg	muscle
30	chr10:52273400-52281000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr10:52273400-52281000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr10:52273400-52282600	Weak transcription	Thymus	Thymus
33	chr10:52273400-52282800	Weak transcription	Spleen	Spleen
34	chr10:52273400-52283800	Weak transcription	Fetal Thymus	thymus
35	chr10:52273400-52286000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr10:52273400-52287000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr10:52273400-52287200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr10:52273600-52286800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr10:52273600-52287400	Weak transcription	GM12878-XiMat	blood
40	chr10:52273600-52289600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:52273600-52298400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:52273600-52299800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr10:52273800-52282400	Weak transcription	Primary T cells from cord blood	blood
44	chr10:52274000-52282200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr10:52274000-52287200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr10:52274800-52288200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr10:52275200-52294200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:52275400-52280400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:52275600-52282600	Weak transcription	Esophagus	oesophagus
50	chr10:52275600-52285000	Weak transcription	Gastric	stomach

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