Variant report

Variant	rs4841196
Chromosome Location	chr8:9555092-9555093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10081478	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10081565	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10099122	0.95[ASN][1000 genomes]
rs10109026	0.86[JPT][hapmap]
rs10794712	0.80[CEU][hapmap]
rs10903317	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11249934	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs11249939	0.94[ASN][1000 genomes]
rs11249942	0.80[CEU][hapmap]
rs11776236	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11779335	0.80[CEU][hapmap];0.85[MKK][hapmap]
rs11785458	0.85[ASN][1000 genomes]
rs12114182	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12155819	0.93[GIH][hapmap];0.92[MKK][hapmap]
rs12541617	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12542457	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12542912	0.86[YRI][hapmap]
rs12543959	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12544371	0.95[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12545250	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12677313	1.00[CEU][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12677507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12679180	1.00[CEU][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12682175	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13250951	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13260526	0.82[CEU][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes]
rs13263409	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13270518	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13270801	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13273033	0.80[CEU][hapmap]
rs13276086	0.93[GIH][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs13282006	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1394	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs35874762	0.86[ASN][1000 genomes]
rs4075359	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4128198	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4240629	0.80[CEU][hapmap]
rs4313162	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4422774	0.84[ASN][1000 genomes]
rs4535744	0.80[CEU][hapmap]
rs4554469	0.80[ASN][1000 genomes]
rs4610751	0.81[CHB][hapmap]
rs4612345	0.81[AMR][1000 genomes]
rs4626603	0.84[CEU][hapmap]
rs4840426	0.93[GIH][hapmap];0.91[JPT][hapmap]
rs4840434	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4840437	0.91[MKK][hapmap]
rs4841203	0.81[AMR][1000 genomes]
rs4841212	0.80[CEU][hapmap]
rs6601338	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6601340	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6601344	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6601350	0.84[AMR][1000 genomes]
rs67711814	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6990300	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6990418	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6994574	0.93[GIH][hapmap];0.88[MKK][hapmap]
rs7003791	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7004937	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7006985	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7010270	0.80[CEU][hapmap]
rs7461376	0.80[CEU][hapmap]
rs7461939	0.93[GIH][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes]
rs7462070	0.81[AMR][1000 genomes]
rs7462910	0.80[CEU][hapmap];0.85[MKK][hapmap]
rs7822700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7840706	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9644704	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9650638	0.80[CEU][hapmap]
rs9650639	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4841196	TNKS	cis	parietal	SCAN
rs4841196	MFHAS1	cis	cerebellum	SCAN
rs4841196	BLK	cis	parietal	SCAN
rs4841196	FLJ10661	cis	cerebellum	SCAN
rs4841196	DEFB134	cis	cerebellum	SCAN
rs4841196	TNKS	cis	cerebellum	SCAN
rs4841196	CTSB	cis	cerebellum	SCAN
rs4841196	PRSS55	cis	cerebellum	SCAN
rs4841196	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9510400-9563800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr8:9511000-9564200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr8:9513200-9564200	Weak transcription	Ovary	ovary
4	chr8:9513200-9567400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:9513400-9605400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:9513800-9563600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr8:9529600-9606400	Weak transcription	Esophagus	oesophagus
8	chr8:9531200-9564000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr8:9534800-9563600	Weak transcription	HepG2	liver
10	chr8:9535000-9564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:9535000-9608000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:9535400-9560800	Weak transcription	HMEC	breast
13	chr8:9535400-9563800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:9536400-9563400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr8:9537400-9563600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr8:9537600-9592400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr8:9540000-9565400	Weak transcription	Fetal Kidney	kidney
18	chr8:9541400-9592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:9541600-9563600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr8:9542200-9606800	Weak transcription	Small Intestine	intestine
21	chr8:9543000-9592200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr8:9543400-9606400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr8:9543800-9563800	Weak transcription	Fetal Stomach	stomach
24	chr8:9543800-9564200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr8:9543800-9564200	Weak transcription	NH-A	brain
26	chr8:9544000-9562800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr8:9544000-9562800	Weak transcription	Left Ventricle	heart
28	chr8:9544000-9586200	Weak transcription	Thymus	Thymus
29	chr8:9544000-9592400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr8:9544000-9592400	Weak transcription	Psoas Muscle	Psoas
31	chr8:9544200-9571200	Weak transcription	Aorta	Aorta
32	chr8:9545400-9560600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr8:9545400-9564400	Weak transcription	HSMM	muscle
34	chr8:9545600-9560600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr8:9545600-9562000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr8:9545600-9563600	Weak transcription	Fetal Muscle Leg	muscle
37	chr8:9545600-9564200	Weak transcription	Osteobl	bone
38	chr8:9545600-9564400	Weak transcription	Fetal Thymus	thymus
39	chr8:9545600-9568600	Weak transcription	HSMMtube	muscle
40	chr8:9545600-9592400	Weak transcription	Brain Angular Gyrus	brain
41	chr8:9545800-9562800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr8:9546000-9555200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr8:9546200-9564200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr8:9546600-9560400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr8:9546600-9563800	Weak transcription	Fetal Intestine Small	intestine
46	chr8:9548000-9562200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr8:9548000-9570600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr8:9548200-9563800	Weak transcription	Placenta	Placenta
49	chr8:9548400-9584400	Weak transcription	Hela-S3	cervix
50	chr8:9548600-9563600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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