Variant report

Variant	rs10509645
Chromosome Location	chr10:94277866-94277867
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:94274603..94278962-chr10:94330841..94335301,9	MCF-7	breast:
2	chr10:94276555..94279204-chr10:94332379..94335098,3	MCF-7	breast:
3	chr10:94276333..94278626-chr10:94332355..94335279,2	K562	blood:

Variant related genes	Relation type
ENSG00000119912	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1044153	0.86[EUR][1000 genomes]
rs10786048	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882067	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882071	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882072	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882074	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882083	0.87[ASN][1000 genomes]
rs10882085	0.86[EUR][1000 genomes]
rs10882092	0.86[EUR][1000 genomes]
rs10882095	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs10882096	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10882099	0.85[CHB][hapmap]
rs11187007	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11187022	1.00[ASN][1000 genomes]
rs11187030	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187072	0.87[ASN][1000 genomes]
rs11187078	1.00[CEU][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11187090	0.86[EUR][1000 genomes]
rs11187096	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs11187098	0.85[EUR][1000 genomes]
rs11187099	0.86[EUR][1000 genomes]
rs11187107	0.85[EUR][1000 genomes]
rs11187114	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs11187117	0.83[EUR][1000 genomes]
rs12220493	0.87[ASN][1000 genomes]
rs12355158	0.85[EUR][1000 genomes]
rs1573051	0.86[EUR][1000 genomes]
rs1972360	0.85[EUR][1000 genomes]
rs2149632	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421943	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2421945	0.82[JPT][hapmap]
rs2798253	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2901597	0.83[ASN][1000 genomes]
rs3781241	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3824735	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs4304670	0.82[JPT][hapmap]
rs61875362	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6583813	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7073833	0.89[ASN][1000 genomes]
rs7076966	0.87[ASN][1000 genomes]
rs7078418	0.85[ASN][1000 genomes]
rs7099761	0.81[JPT][hapmap]
rs7921210	0.82[ASN][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	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv551924	chr10:94212742-94290484	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv551925	chr10:94224165-94288429	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1802816	chr10:94232247-94294291	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1792868	chr10:94232247-94409749	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv895894	chr10:94249982-94452430	Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10509645	STAMBPL1	cis	cerebellum	SCAN
rs10509645	KIF11	cis	cerebellum	SCAN
rs10509645	NOC3L	cis	cerebellum	SCAN
rs10509645	HECTD2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94239600-94280400	Weak transcription	Fetal Brain Male	brain
2	chr10:94244000-94303000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:94250200-94289400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:94250200-94295200	Weak transcription	Pancreas	Pancrea
5	chr10:94250200-94297200	Weak transcription	Brain Germinal Matrix	brain
6	chr10:94250200-94313800	Weak transcription	Brain Substantia Nigra	brain
7	chr10:94250400-94301000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr10:94250400-94307400	Weak transcription	Spleen	Spleen
9	chr10:94252600-94302200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:94257600-94289400	Weak transcription	Right Ventricle	heart
11	chr10:94259400-94289000	Weak transcription	NH-A	brain
12	chr10:94260000-94296800	Weak transcription	Esophagus	oesophagus
13	chr10:94262000-94289200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr10:94262000-94297600	Weak transcription	Psoas Muscle	Psoas
15	chr10:94262000-94307400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr10:94264200-94295000	Weak transcription	Small Intestine	intestine
17	chr10:94265800-94290400	Weak transcription	Osteobl	bone
18	chr10:94267200-94283000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:94267600-94297400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:94267600-94314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:94267800-94328800	Weak transcription	Fetal Heart	heart
22	chr10:94268000-94313800	Weak transcription	Colon Smooth Muscle	Colon
23	chr10:94268000-94313800	Weak transcription	NHLF	lung
24	chr10:94268600-94290800	Weak transcription	Fetal Lung	lung
25	chr10:94268600-94295200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr10:94268600-94300000	Weak transcription	Colonic Mucosa	Colon
27	chr10:94268800-94290000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:94269000-94290200	Weak transcription	Fetal Kidney	kidney
29	chr10:94269400-94314000	Weak transcription	Aorta	Aorta
30	chr10:94269600-94287400	Weak transcription	Fetal Intestine Small	intestine
31	chr10:94269600-94289200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:94269600-94289200	Weak transcription	Fetal Stomach	stomach
33	chr10:94269600-94314000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:94269800-94290000	Weak transcription	Ovary	ovary
35	chr10:94269800-94295000	Weak transcription	Lung	lung
36	chr10:94270000-94289200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr10:94270200-94289400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:94272000-94286200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:94272000-94288800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr10:94272000-94317200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr10:94272200-94282800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:94272200-94288600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:94272200-94288800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr10:94272200-94288800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr10:94272200-94289000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr10:94272200-94289000	Weak transcription	NHEK	skin
47	chr10:94272200-94289200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr10:94272200-94289200	Weak transcription	Left Ventricle	heart
49	chr10:94272200-94289400	Weak transcription	Fetal Muscle Leg	muscle
50	chr10:94272200-94289400	Weak transcription	HepG2	liver

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