Variant report

Variant	rs10804442
Chromosome Location	chr3:105519212-105519213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10933833	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711088	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12636287	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13060223	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13100446	0.94[AMR][1000 genomes]
rs1443102	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470283	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1550711	0.94[ASW][hapmap];0.83[YRI][hapmap]
rs1867191	0.94[ASW][hapmap];0.86[YRI][hapmap]
rs1867195	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992522	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2055557	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2099892	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2120105	0.80[GIH][hapmap]
rs2399056	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427229	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28533328	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3996189	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4243427	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4447799	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894950	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894953	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894954	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4894957	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894960	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894962	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6437624	0.94[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6788366	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6795961	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807382	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71627856	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs726443	0.94[ASW][hapmap]
rs7432372	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637327	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645021	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7647955	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651784	0.94[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs769315	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971110	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9841500	0.94[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10804442	CBLB	cis	cerebellum	SCAN
rs10804442	ALCAM	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
4	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:105509800-105527800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:105510600-105521200	Weak transcription	Fetal Brain Male	brain
7	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
8	chr3:105511800-105520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:105512000-105520600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:105512200-105520200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:105512200-105520400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
14	chr3:105512400-105524400	Weak transcription	NHLF	lung
15	chr3:105512600-105520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:105512600-105524000	Weak transcription	HSMMtube	muscle
17	chr3:105512600-105524600	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:105512600-105525200	Weak transcription	HSMM	muscle
19	chr3:105514400-105521600	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:105515400-105528200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:105515400-105539000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:105515800-105521600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr3:105516000-105519400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:105516000-105521600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:105516000-105521600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:105516200-105522200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:105516400-105519400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:105516400-105521000	Enhancers	Primary T cells from cord blood	blood
29	chr3:105516400-105521800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:105516600-105519400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:105516600-105519400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:105516600-105519800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:105516600-105522000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:105516600-105523000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:105516800-105519800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr3:105517200-105519400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:105517400-105519600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:105517400-105519800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:105517800-105519600	Genic enhancers	Osteobl	bone
40	chr3:105517800-105519800	Weak transcription	Fetal Heart	heart
41	chr3:105517800-105520400	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:105517800-105520800	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:105517800-105521000	Weak transcription	NH-A	brain
44	chr3:105517800-105522000	Enhancers	Primary B cells from cord blood	blood
45	chr3:105517800-105522200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:105517800-105524800	Weak transcription	A549	lung
47	chr3:105517800-105525400	Weak transcription	Fetal Intestine Large	intestine
48	chr3:105517800-105527800	Weak transcription	Fetal Kidney	kidney
49	chr3:105517800-105528200	Weak transcription	Brain Substantia Nigra	brain
50	chr3:105517800-105528400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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