Variant report

Variant	rs1938777
Chromosome Location	chr11:73122340-73122341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:73111818..73115266-chr11:73122319..73124692,3	K562	blood:
2	chr11:73103434..73107265-chr11:73121056..73124358,3	MCF-7	breast:
3	chr11:73120640..73123438-chr11:73131254..73134143,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054967	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1002126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1002127	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10501411	0.89[CEU][hapmap]
rs11235738	1.00[JPT][hapmap]
rs11235745	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11235759	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11235770	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11235775	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235809	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs11544310	0.90[EUR][1000 genomes]
rs11544311	0.80[EUR][1000 genomes]
rs11820929	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11821094	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11823913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11823923	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11824614	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11826896	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11826909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11828904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12269884	1.00[JPT][hapmap]
rs12274589	1.00[JPT][hapmap]
rs12275766	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12276892	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs12282282	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12282790	1.00[JPT][hapmap]
rs12285885	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12288753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12290623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12290835	1.00[JPT][hapmap]
rs17244596	1.00[CEU][hapmap]
rs17244602	1.00[CEU][hapmap]
rs17244616	1.00[CEU][hapmap]
rs17310361	1.00[CEU][hapmap]
rs17310374	1.00[CEU][hapmap]
rs17851510	1.00[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs1894076	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2027760	0.89[CEU][hapmap]
rs2027761	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs2027763	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2298469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298807	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28641751	0.92[ASN][1000 genomes]
rs3741149	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3741152	0.89[CEU][hapmap]
rs3825005	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3933402	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs5004964	0.86[AMR][1000 genomes]
rs61345051	0.80[EUR][1000 genomes]
rs61516411	0.80[AMR][1000 genomes]
rs6592521	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7101831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7102197	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7105681	0.89[CEU][hapmap]
rs7110369	0.89[CEU][hapmap]
rs7112924	0.90[EUR][1000 genomes]
rs7113420	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7114009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7114376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7115055	1.00[CEU][hapmap]
rs7115806	0.89[CEU][hapmap]
rs7118982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7122825	0.89[CEU][hapmap]
rs7123298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7123985	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs7125598	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7125949	0.89[CEU][hapmap]
rs7125978	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7129990	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7131383	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7131397	1.00[JPT][hapmap]
rs724111	1.00[CEU][hapmap]
rs725103	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7342205	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs73542952	0.80[EUR][1000 genomes]
rs73542960	0.80[EUR][1000 genomes]
rs73542967	0.80[EUR][1000 genomes]
rs73542976	0.80[EUR][1000 genomes]
rs73542979	0.80[EUR][1000 genomes]
rs73542990	0.80[EUR][1000 genomes]
rs7925226	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7927344	0.84[AMR][1000 genomes]
rs7930454	0.89[CEU][hapmap]
rs7930880	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7934218	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes]
rs7935948	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs7937066	0.88[ASN][1000 genomes]
rs7938391	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs7941359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7944099	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7944346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7945825	1.00[CEU][hapmap]
rs7951072	1.00[CEU][hapmap]
rs7951174	0.81[ASN][1000 genomes]
rs7952686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs876480	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs880317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs947837	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9888218	1.00[JPT][hapmap]

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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1938777	ARHGEF17	cis	Whole Blood	GTEx
rs1938777	P2RY2	cis	cerebellum	SCAN
rs1938777	CCND1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73096200-73130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:73098600-73126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:73098600-73132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr11:73099200-73139800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:73099200-73141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:73101200-73124800	Weak transcription	Psoas Muscle	Psoas
7	chr11:73104600-73123400	Strong transcription	Fetal Stomach	stomach
8	chr11:73104800-73122600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:73110600-73123200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:73110800-73123000	Weak transcription	HUVEC	blood vessel
11	chr11:73110800-73123200	Weak transcription	NH-A	brain
12	chr11:73110800-73124000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:73111400-73123200	Strong transcription	Thymus	Thymus
14	chr11:73112800-73123400	Strong transcription	Brain Germinal Matrix	brain
15	chr11:73113000-73126200	Weak transcription	Small Intestine	intestine
16	chr11:73113400-73125000	Weak transcription	Right Atrium	heart
17	chr11:73113600-73132600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr11:73113800-73122800	Strong transcription	Fetal Intestine Small	intestine
19	chr11:73114600-73123000	Strong transcription	Fetal Thymus	thymus
20	chr11:73114600-73125200	Strong transcription	Primary T cells from cord blood	blood
21	chr11:73114800-73122800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:73115200-73126200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:73115200-73132200	Weak transcription	Fetal Heart	heart
24	chr11:73115200-73132400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:73115200-73149400	Weak transcription	Fetal Kidney	kidney
26	chr11:73115600-73122800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:73115800-73122400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr11:73115800-73122600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:73116000-73123000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:73116000-73123000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:73116000-73123000	Strong transcription	Dnd41	blood
32	chr11:73116200-73122600	Strong transcription	Lung	lung
33	chr11:73116200-73122800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:73116200-73123200	Strong transcription	Fetal Brain Female	brain
35	chr11:73116200-73124200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr11:73116400-73123000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr11:73116600-73122400	Strong transcription	Pancreas	Pancrea
38	chr11:73116600-73122800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:73116600-73126600	Weak transcription	Stomach Mucosa	stomach
40	chr11:73116800-73132600	Strong transcription	Primary B cells from cord blood	blood
41	chr11:73117000-73122800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr11:73117000-73123000	Strong transcription	Fetal Muscle Leg	muscle
43	chr11:73117000-73123200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:73117000-73123400	Weak transcription	HSMM	muscle
45	chr11:73117000-73131400	Weak transcription	A549	lung
46	chr11:73117800-73130200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:73118800-73128200	Weak transcription	Fetal Brain Male	brain
48	chr11:73118800-73137600	Weak transcription	Colonic Mucosa	Colon
49	chr11:73119000-73122400	Strong transcription	NHEK	skin
50	chr11:73119000-73123200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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