Variant report

Variant	rs6795961
Chromosome Location	chr3:105524643-105524644
allele	A/G
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]
rs10804442	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]
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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.94[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];0.97[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];0.96[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	1.00[ASW][hapmap];0.83[YRI][hapmap]
rs1867191	1.00[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	0.83[ASW][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];0.97[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];0.97[ASN][1000 genomes]
rs4894953	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[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]
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	1.00[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	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[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	1.00[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];1.00[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];0.97[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	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[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
rs6795961	ALCAM	cis	cerebellum	SCAN
rs6795961	CBLB	cis	cerebellum	SCAN

Chromatin state (count:77 , 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	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
7	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
9	chr3:105512600-105525200	Weak transcription	HSMM	muscle
10	chr3:105515400-105528200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:105515400-105539000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:105517800-105524800	Weak transcription	A549	lung
13	chr3:105517800-105525400	Weak transcription	Fetal Intestine Large	intestine
14	chr3:105517800-105527800	Weak transcription	Fetal Kidney	kidney
15	chr3:105517800-105528200	Weak transcription	Brain Substantia Nigra	brain
16	chr3:105517800-105528400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:105518400-105525600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:105518400-105525800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:105519200-105541600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:105519400-105524800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:105519400-105527800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:105520600-105525200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:105520800-105525200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:105520800-105531400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:105521200-105525000	Weak transcription	NHDF-Ad	bronchial
26	chr3:105521200-105525800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:105521200-105527800	Weak transcription	Fetal Lung	lung
28	chr3:105521200-105530200	Weak transcription	HMEC	breast
29	chr3:105521200-105531200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:105521200-105536000	Weak transcription	Right Ventricle	heart
31	chr3:105521200-105546800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:105521400-105525400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:105521400-105528200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:105521400-105529200	Weak transcription	Psoas Muscle	Psoas
35	chr3:105521400-105530200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:105521400-105541200	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:105521400-105542000	Weak transcription	Fetal Stomach	stomach
38	chr3:105521600-105528000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:105521600-105530200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:105521800-105525200	Weak transcription	HepG2	liver
41	chr3:105522000-105527000	Weak transcription	Primary B cells from cord blood	blood
42	chr3:105522200-105524800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:105522200-105524800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:105522200-105528400	Weak transcription	Fetal Heart	heart
45	chr3:105522400-105525000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:105522400-105526600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:105522400-105529800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:105522400-105533800	Weak transcription	Brain Germinal Matrix	brain
49	chr3:105522400-105541200	Weak transcription	Primary T cells from cord blood	blood
50	chr3:105523000-105525400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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