Variant report

Variant	rs7068398
Chromosome Location	chr10:49527206-49527207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49521352..49523336-chr10:49525109..49528054,2	MCF-7	breast:
2	chr10:49513964..49516103-chr10:49525788..49528265,2	MCF-7	breast:
3	chr10:49525579..49528605-chr10:49532871..49535905,3	K562	blood:
4	chr10:49525748..49527877-chr10:49536971..49539943,2	K562	blood:
5	chr10:49525969..49527721-chr10:49529565..49532271,2	K562	blood:
6	chr10:49527138..49528910-chr10:49653802..49655584,2	K562	blood:

Variant related genes	Relation type
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10745265	0.93[JPT][hapmap]
rs10776592	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10776593	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10776594	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10857563	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10857564	1.00[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10857565	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11101284	0.86[GIH][hapmap]
rs11101285	0.94[JPT][hapmap]
rs11101326	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs1112268	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11597435	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11598320	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12358297	1.00[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17780725	1.00[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1881735	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1881737	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1881738	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1881740	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1881741	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1919706	1.00[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1919707	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1919709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1997365	0.94[JPT][hapmap]
rs2141516	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2178339	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2377140	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2377141	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2377143	0.88[JPT][hapmap]
rs2377349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2590382	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2590383	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2590384	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2590385	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2590386	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2590391	1.00[CEU][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2698758	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2698762	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2698768	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2889595	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3813864	0.83[CEU][hapmap]
rs4012930	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4838404	0.82[JPT][hapmap]
rs4838405	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4838588	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56078229	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6537559	0.94[JPT][hapmap]
rs7084326	0.85[EUR][1000 genomes]
rs7898026	0.88[JPT][hapmap]
rs9919504	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats 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
5	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv6587	chr10:49526329-49571804	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7068398	MSMB	cis	parietal	SCAN
rs7068398	ANTXRL	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49515600-49541400	Weak transcription	Lung	lung
2	chr10:49516400-49528000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr10:49516400-49528600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:49516400-49535000	Weak transcription	Fetal Muscle Leg	muscle
5	chr10:49516400-49538400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr10:49516400-49538800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:49516400-49541400	Weak transcription	Right Atrium	heart
8	chr10:49516400-49547200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:49516400-49559600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:49516600-49538400	Weak transcription	Primary B cells from cord blood	blood
11	chr10:49516600-49538600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:49516600-49538600	Weak transcription	Fetal Stomach	stomach
13	chr10:49517800-49544600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:49518000-49528800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:49518000-49536000	Weak transcription	Fetal Intestine Small	intestine
16	chr10:49518200-49527600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:49518200-49542200	Weak transcription	HSMM	muscle
18	chr10:49518600-49538400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr10:49518800-49534400	Weak transcription	Brain Germinal Matrix	brain
20	chr10:49518800-49538600	Weak transcription	Fetal Intestine Large	intestine
21	chr10:49518800-49540600	Weak transcription	NHEK	skin
22	chr10:49518800-49542000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:49518800-49544000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr10:49519000-49530600	Weak transcription	Fetal Brain Male	brain
25	chr10:49519000-49538600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr10:49519000-49540200	Weak transcription	HMEC	breast
27	chr10:49519400-49529600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr10:49519400-49532200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:49520200-49549800	Weak transcription	HUVEC	blood vessel
30	chr10:49520800-49527800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr10:49520800-49532000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr10:49521000-49536400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:49522800-49539200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr10:49522800-49550800	Weak transcription	Small Intestine	intestine
35	chr10:49523400-49535600	Weak transcription	Primary T cells from cord blood	blood
36	chr10:49523400-49538400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:49523600-49538600	Weak transcription	Colon Smooth Muscle	Colon
38	chr10:49524800-49538400	Weak transcription	Right Ventricle	heart
39	chr10:49525000-49541600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr10:49525200-49535400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:49525400-49538400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr10:49525800-49528800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr10:49525800-49530600	Weak transcription	Left Ventricle	heart
44	chr10:49525800-49551800	Weak transcription	Adipose Nuclei	Adipose
45	chr10:49526000-49527800	Weak transcription	K562	blood
46	chr10:49526000-49530400	Weak transcription	Psoas Muscle	Psoas
47	chr10:49526000-49531200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr10:49526000-49537200	Weak transcription	Thymus	Thymus
49	chr10:49526000-49538400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr10:49526000-49538400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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