Variant report

Variant	rs1944971
Chromosome Location	chr11:73923418-73923419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10219237	0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10431176	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10501415	0.95[CHB][hapmap]
rs10898955	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs10898957	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs10898958	0.82[ASN][1000 genomes]
rs10898959	0.83[ASN][1000 genomes]
rs10898960	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs10898961	0.91[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10898962	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898963	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10898964	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898966	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898974	0.82[EUR][1000 genomes]
rs10898975	0.83[CEU][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10898976	0.83[CEU][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10898980	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs1095423	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs11235979	0.83[YRI][hapmap]
rs11235994	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs11235995	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs11235996	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs11235998	0.82[EUR][1000 genomes]
rs11235999	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs11236000	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap]
rs11236003	0.95[CHB][hapmap]
rs11236016	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11236020	0.83[ASN][1000 genomes]
rs11236026	0.88[ASN][1000 genomes]
rs11236027	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs11236029	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236042	0.83[CEU][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11236043	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11236044	0.82[EUR][1000 genomes]
rs11236052	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs11236053	0.83[CEU][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11236054	0.81[EUR][1000 genomes]
rs11236063	0.83[CEU][hapmap]
rs11236071	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs11236077	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs11236092	0.83[CEU][hapmap]
rs11600314	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11601582	0.82[ASN][1000 genomes]
rs11602451	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11604125	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs11604713	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[ASN][1000 genomes]
rs11606804	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs11607335	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs11608147	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs12222213	0.88[ASN][1000 genomes]
rs12223320	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs12225446	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12285706	1.00[YRI][hapmap]
rs12291461	0.83[YRI][hapmap]
rs12574038	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs12574039	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12574047	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs12574556	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12574650	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12574824	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12574898	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12574960	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12575211	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1405653	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1405654	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1527302	0.88[CHB][hapmap]
rs1617256	0.83[YRI][hapmap]
rs1618253	0.83[YRI][hapmap]
rs1685333	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs1685341	0.83[YRI][hapmap]
rs1685342	0.95[YRI][hapmap]
rs1685343	0.83[YRI][hapmap]
rs17132602	0.83[YRI][hapmap]
rs17132701	0.81[EUR][1000 genomes]
rs17132715	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs17132964	0.83[CEU][hapmap]
rs1726755	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs1726756	0.95[YRI][hapmap]
rs1790383	1.00[YRI][hapmap]
rs1790408	1.00[YRI][hapmap]
rs1790409	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2091436	0.86[ASN][1000 genomes]
rs2178000	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[ASN][1000 genomes]
rs2282488	0.83[CEU][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2302508	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950412	1.00[YRI][hapmap]
rs35826958	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741132	0.83[CEU][hapmap];0.87[CHD][hapmap]
rs3741133	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3814724	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3819114	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4019299	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs4539349	0.91[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4565925	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs59109060	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60834556	0.83[ASN][1000 genomes]
rs61901238	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61901245	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61901246	0.82[ASN][1000 genomes]
rs61901247	0.82[ASN][1000 genomes]
rs61901248	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61901252	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61902362	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7110734	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.83[ASN][1000 genomes]
rs7115146	0.85[ASN][1000 genomes]
rs7115407	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs7117465	0.87[CHD][hapmap]
rs7119710	0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7125032	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs7935920	0.80[ASN][1000 genomes]
rs7949639	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7951239	0.82[ASN][1000 genomes]
rs7951290	0.88[ASN][1000 genomes]
rs7951617	0.83[CEU][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7951743	0.83[ASN][1000 genomes]
rs7952669	0.82[ASN][1000 genomes]
rs826041	1.00[YRI][hapmap]
rs826043	1.00[YRI][hapmap]
rs826044	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs826045	1.00[YRI][hapmap]
rs826046	1.00[YRI][hapmap]
rs826047	1.00[YRI][hapmap]
rs826049	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs826070	0.95[YRI][hapmap]
rs826074	0.95[YRI][hapmap]
rs826076	1.00[YRI][hapmap]
rs826077	1.00[YRI][hapmap]
rs826086	1.00[YRI][hapmap]
rs826088	1.00[YRI][hapmap]
rs826090	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1944971	PPME1	cis	cerebellum	SCAN
rs1944971	DGAT2	cis	parietal	SCAN
rs1944971	DNAJB13	cis	cerebellum	SCAN
rs1944971	FAM168A	cis	parietal	SCAN
rs1944971	STARD10	cis	parietal	SCAN
rs1944971	P4HA3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73884200-73941200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:73884200-73941800	Weak transcription	Small Intestine	intestine
3	chr11:73885600-73925600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr11:73885600-73957000	Weak transcription	Fetal Brain Male	brain
5	chr11:73885800-73942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:73891400-73924000	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:73897200-73937600	Weak transcription	Fetal Heart	heart
8	chr11:73901600-73938000	Weak transcription	Psoas Muscle	Psoas
9	chr11:73902200-73936200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr11:73902600-73941200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:73903800-73923600	Weak transcription	Right Ventricle	heart
12	chr11:73905200-73941800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:73907400-73941200	Weak transcription	NHDF-Ad	bronchial
14	chr11:73907400-73969200	Weak transcription	HUVEC	blood vessel
15	chr11:73909400-73928200	Strong transcription	HSMM	muscle
16	chr11:73913200-73941200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:73913600-73946800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:73913800-73961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:73914800-73927000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:73915000-73924000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:73915000-73924200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr11:73915000-73926400	Strong transcription	HSMMtube	muscle
23	chr11:73915000-73927200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:73915200-73924600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:73915600-73941200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:73915600-73960600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:73916000-73957000	Weak transcription	NHLF	lung
28	chr11:73916800-73939800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:73918000-73924400	Strong transcription	Fetal Intestine Large	intestine
30	chr11:73918000-73942000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:73918200-73942400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:73918400-73936400	Weak transcription	Ovary	ovary
33	chr11:73918800-73925600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr11:73919800-73924600	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr11:73920000-73924600	Strong transcription	A549	lung
36	chr11:73920800-73941200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:73921200-73924200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:73921400-73923800	Weak transcription	Fetal Thymus	thymus
39	chr11:73921600-73923600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:73921600-73924400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr11:73921600-73941200	Weak transcription	Osteobl	bone
42	chr11:73921800-73923800	Weak transcription	Brain Anterior Caudate	brain
43	chr11:73921800-73923800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:73921800-73924200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:73921800-73926400	Weak transcription	NH-A	brain
46	chr11:73921800-73941200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:73921800-73941200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:73921800-73942400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:73921800-73949800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr11:73921800-73950200	Weak transcription	Fetal Kidney	kidney

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