Variant report

Variant	rs4681994
Chromosome Location	chr3:56715363-56715364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:56707072..56708805-chr3:56713391..56715863,2	K562	blood:
2	chr3:56705021..56708606-chr3:56714722..56718211,5	MCF-7	breast:
3	chr3:56690378..56691903-chr3:56713310..56716081,2	K562	blood:
4	chr3:56714433..56716910-chr3:57020526..57023323,2	MCF-7	breast:
5	chr3:56715125..56717534-chr4:38104477..38107344,2	MCF-7	breast:
6	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:

Variant related genes	Relation type
ENSG00000065882	Chromatin interaction
ENSG00000180376	Chromatin interaction
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10049468	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11130537	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130540	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11130541	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17235670	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2317134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2317244	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2317252	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282523	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs282528	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs282536	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282541	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4234393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681725	0.82[EUR][1000 genomes]
rs4681734	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4681740	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4681933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681964	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4681980	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682000	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55831745	0.82[ASN][1000 genomes]
rs55938093	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56190096	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs56204053	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62251242	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6445801	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445803	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445804	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445810	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6778373	0.82[ASN][1000 genomes]
rs6781056	0.82[ASN][1000 genomes]
rs6781293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs6787227	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs6802498	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6809499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73079902	0.82[ASN][1000 genomes]
rs73081810	0.82[ASN][1000 genomes]
rs73081811	0.82[ASN][1000 genomes]
rs73081819	0.82[ASN][1000 genomes]
rs73081823	0.82[ASN][1000 genomes]
rs73081825	0.82[ASN][1000 genomes]
rs73081851	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73081854	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617331	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7618007	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7619465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7620259	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7631662	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7642389	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs958755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9809309	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9833926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9835332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9839065	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851653	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9858568	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9875257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9878373	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4681994	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL
rs4681994	CCDC66	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56675800-56716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:56695400-56716000	Weak transcription	Fetal Brain Male	brain
3	chr3:56695600-56715600	Weak transcription	Stomach Mucosa	stomach
4	chr3:56699600-56716000	Weak transcription	Fetal Kidney	kidney
5	chr3:56699600-56716200	Weak transcription	Spleen	Spleen
6	chr3:56699800-56716000	Weak transcription	Aorta	Aorta
7	chr3:56701800-56716000	Weak transcription	Psoas Muscle	Psoas
8	chr3:56702400-56715400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:56702400-56716200	Weak transcription	Small Intestine	intestine
10	chr3:56702600-56715800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:56702600-56716000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:56702600-56716000	Weak transcription	Colonic Mucosa	Colon
13	chr3:56702800-56715800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:56703000-56716200	Weak transcription	Ovary	ovary
15	chr3:56703200-56716000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:56703600-56715400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:56704800-56715600	Weak transcription	HSMMtube	muscle
18	chr3:56704800-56715800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:56704800-56716000	Weak transcription	Brain Germinal Matrix	brain
20	chr3:56704800-56716200	Weak transcription	Left Ventricle	heart
21	chr3:56705200-56716000	Weak transcription	Fetal Lung	lung
22	chr3:56705200-56716000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:56705200-56716200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:56705400-56715400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:56705400-56716000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:56705400-56716000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:56705400-56716200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:56705400-56716200	Weak transcription	Gastric	stomach
29	chr3:56705800-56715400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:56705800-56715400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:56706200-56715800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:56707200-56715400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:56707200-56716000	Weak transcription	Fetal Intestine Large	intestine
34	chr3:56707200-56716200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:56707200-56716200	Weak transcription	Esophagus	oesophagus
36	chr3:56707400-56715400	Weak transcription	Brain Anterior Caudate	brain
37	chr3:56707400-56716000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:56707400-56716000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:56707400-56716000	Weak transcription	Fetal Intestine Small	intestine
40	chr3:56708000-56715400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:56709600-56715400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:56709800-56715400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:56710800-56715400	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr3:56711000-56715600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr3:56711200-56716000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:56711800-56715400	Weak transcription	Brain Angular Gyrus	brain
47	chr3:56712800-56715600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:56713000-56715400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:56713000-56716000	Weak transcription	Fetal Stomach	stomach
50	chr3:56713000-56716200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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