Variant report

Variant	rs2305638
Chromosome Location	chr3:47046842-47046843
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47046776-47047305	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:47046330-47047263	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:47046577-47047031	K562	blood:	n/a	n/a
4	POLR2A	chr3:47046229-47046928	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:47046784-47047144	K562	blood:	n/a	n/a
6	POLR2A	chr3:47046705-47047104	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:47046496-47046868	HL-60	blood:	n/a	n/a
8	POLR2A	chr3:47046526-47050420	GM12892	blood:	n/a	n/a
9	POLR2A	chr3:47046231-47047105	K562	blood:	n/a	n/a
10	POLR2A	chr3:47046668-47046945	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:47046195-47047213	K562	blood:	n/a	n/a
12	POLR2A	chr3:47046638-47046900	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
NBEAL2	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10433549	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10461018	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1079276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1108301	0.91[EUR][1000 genomes]
rs11130110	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11130111	0.88[CEU][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130112	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11130115	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11709660	0.82[EUR][1000 genomes]
rs11715121	0.82[EUR][1000 genomes]
rs11716553	0.86[EUR][1000 genomes]
rs11719795	0.81[JPT][hapmap]
rs11720139	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs11917361	0.81[EUR][1000 genomes]
rs11917474	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12152493	0.90[EUR][1000 genomes]
rs12491473	0.88[EUR][1000 genomes]
rs12630534	0.88[EUR][1000 genomes]
rs12715421	0.81[EUR][1000 genomes]
rs13061071	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13062681	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13066214	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077398	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13087426	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13091054	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13098228	0.80[ASN][1000 genomes]
rs1463393	0.88[EUR][1000 genomes]
rs17784127	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1869869	0.92[EUR][1000 genomes]
rs1869871	0.84[EUR][1000 genomes]
rs2061197	0.88[CEU][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278963	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs2290546	0.82[JPT][hapmap]
rs2305634	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305635	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs2385867	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34103310	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34344887	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4078466	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4082155	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4234465	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs4587	0.82[JPT][hapmap]
rs4682831	0.91[EUR][1000 genomes]
rs4682837	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs4682844	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs4682852	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs4683297	0.81[JPT][hapmap]
rs4683298	0.81[JPT][hapmap]
rs4683322	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs55724164	0.83[EUR][1000 genomes]
rs55843455	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55927279	0.81[EUR][1000 genomes]
rs56217494	0.85[EUR][1000 genomes]
rs56249396	0.83[EUR][1000 genomes]
rs61729713	0.91[EUR][1000 genomes]
rs62246375	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62246398	0.83[EUR][1000 genomes]
rs62248439	0.88[EUR][1000 genomes]
rs6442040	0.81[JPT][hapmap]
rs6442055	0.80[EUR][1000 genomes]
rs66539935	0.91[EUR][1000 genomes]
rs66564457	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6763236	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6767218	0.83[EUR][1000 genomes]
rs6767907	0.84[CEU][hapmap]
rs6768722	0.82[EUR][1000 genomes]
rs6772670	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6774733	0.89[EUR][1000 genomes]
rs6777145	0.80[EUR][1000 genomes]
rs6794193	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808742	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433300	0.80[CEU][hapmap]
rs749511	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs749512	0.80[CEU][hapmap]
rs7610636	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617689	0.88[EUR][1000 genomes]
rs7621911	0.83[ASN][1000 genomes]
rs7625067	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625070	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7628747	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs7633698	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636252	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637302	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7640397	0.89[EUR][1000 genomes]
rs7645278	0.81[JPT][hapmap]
rs9311403	0.88[CEU][hapmap]
rs9837343	0.84[CEU][hapmap]
rs9844122	0.81[EUR][1000 genomes]
rs9845728	0.81[EUR][1000 genomes]
rs9852082	0.81[JPT][hapmap]
rs9854790	0.80[EUR][1000 genomes]
rs9855938	0.81[JPT][hapmap]
rs9858443	0.81[EUR][1000 genomes]
rs9875235	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
7	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2305638	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs2305638	RTP3	cis	lesional skin	skin_eQTL
rs2305638	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
2	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:47029800-47050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:47031000-47049600	Strong transcription	Gastric	stomach
5	chr3:47031000-47050200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:47031000-47053000	Strong transcription	Dnd41	blood
7	chr3:47032200-47050000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:47033800-47049200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:47034200-47049800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:47035400-47049000	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:47038000-47050000	Strong transcription	Thymus	Thymus
12	chr3:47038600-47050000	Strong transcription	Fetal Stomach	stomach
13	chr3:47038600-47050400	Weak transcription	Fetal Lung	lung
14	chr3:47039000-47050000	Strong transcription	Adipose Nuclei	Adipose
15	chr3:47039800-47050200	Strong transcription	Colonic Mucosa	Colon
16	chr3:47039800-47058000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:47040000-47049400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:47040000-47050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:47040200-47049000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:47040200-47049000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr3:47040200-47049800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:47040200-47049800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:47040400-47048800	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:47040400-47049200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr3:47040400-47049600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:47040400-47050000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:47040400-47050000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:47040400-47050000	Strong transcription	Spleen	Spleen
29	chr3:47040400-47050400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:47040400-47050400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:47040400-47050400	Weak transcription	Right Atrium	heart
32	chr3:47040600-47048000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:47040600-47048200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr3:47040600-47048400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr3:47040600-47049600	Strong transcription	Right Ventricle	heart
36	chr3:47040600-47049800	Strong transcription	Primary T cells from cord blood	blood
37	chr3:47040600-47049800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:47040600-47050000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:47040600-47050200	Strong transcription	Stomach Mucosa	stomach
40	chr3:47040600-47050400	Weak transcription	Fetal Kidney	kidney
41	chr3:47040600-47051000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:47040600-47051400	Weak transcription	Fetal Heart	heart
43	chr3:47040800-47048200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:47040800-47048400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:47040800-47048400	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:47040800-47049000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:47040800-47049200	Strong transcription	Liver	Liver
48	chr3:47040800-47049600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:47040800-47050200	Strong transcription	Fetal Intestine Small	intestine
50	chr3:47040800-47050200	Strong transcription	Rectal Mucosa Donor 29	rectum

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