Variant report

Variant	rs940174
Chromosome Location	chr3:136309710-136309711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136309554..136311362-chr3:136314085..136316749,2	K562	blood:
2	chr3:136309415..136311669-chr3:136473283..136476207,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1017882	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10513014	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1070232	0.93[JPT][hapmap]
rs10935182	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs10935183	0.96[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs10935184	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10935185	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1145106	0.87[JPT][hapmap]
rs11715257	0.87[JPT][hapmap]
rs11717954	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11919030	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12163529	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12492510	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12630999	0.93[JPT][hapmap]
rs12635723	0.93[JPT][hapmap]
rs1394092	0.93[JPT][hapmap]
rs1681817	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1729951	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2062322	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2655008	0.87[JPT][hapmap]
rs2688600	0.85[AMR][1000 genomes]
rs2688601	0.85[AMR][1000 genomes]
rs34438032	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3856637	0.93[JPT][hapmap]
rs4038578	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4038587	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4408829	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs4521165	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4630889	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4678433	0.93[JPT][hapmap]
rs4678436	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4678437	0.93[JPT][hapmap]
rs4678438	0.93[JPT][hapmap]
rs55970317	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6439649	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6439655	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs6789329	0.92[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs6791142	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6791611	0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs6794351	0.93[JPT][hapmap]
rs6802702	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6808312	0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs696518	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs699165	0.93[JPT][hapmap]
rs711975	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs73228043	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7427564	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7432375	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7616204	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7618518	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7618871	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7620314	0.92[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs7621025	0.93[JPT][hapmap]
rs7634476	0.81[ASN][1000 genomes]
rs7637129	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs833752	0.93[JPT][hapmap]
rs834304	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs864437	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs866758	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs900048	0.87[JPT][hapmap]
rs900818	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9836231	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9845762	0.93[JPT][hapmap]
rs9854084	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv1794138	chr3:136300732-136332204	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs940174	DBR1	cis	cerebellum	SCAN
rs940174	PCCB	cis	parietal	SCAN
rs940174	PCCB	cis	lymphoblastoid	seeQTL
rs940174	PCCB	cis	multi-tissue	Pritchard
rs940174	PCCB	cis	cerebellum	SCAN
rs940174	SPSB4	cis	cerebellum	SCAN
rs940174	MSL2	cis	parietal	SCAN
rs940174	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
6	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:136251600-136322400	Weak transcription	Liver	Liver
9	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:136265400-136314800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:136266400-136315600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:136266600-136314600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:136266600-136316200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:136266800-136314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
18	chr3:136271200-136331400	Weak transcription	NHDF-Ad	bronchial
19	chr3:136272600-136335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:136274200-136314000	Weak transcription	GM12878-XiMat	blood
21	chr3:136277800-136315200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:136280000-136323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:136283600-136314600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:136283800-136341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:136284400-136337800	Weak transcription	Fetal Kidney	kidney
26	chr3:136285000-136314800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:136285200-136335400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:136285400-136313600	Weak transcription	Left Ventricle	heart
29	chr3:136286600-136314600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:136286800-136322600	Weak transcription	Placenta	Placenta
31	chr3:136286800-136343600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:136287200-136335400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:136289600-136341800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:136290000-136351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:136290400-136315000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:136294400-136314600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:136294800-136319600	Weak transcription	Fetal Lung	lung
38	chr3:136297200-136345400	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:136297200-136351200	Weak transcription	Pancreas	Pancrea
40	chr3:136297600-136314600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:136297800-136315600	Weak transcription	Psoas Muscle	Psoas
42	chr3:136298200-136311800	Weak transcription	Colonic Mucosa	Colon
43	chr3:136298400-136313600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:136298400-136314000	Weak transcription	HUVEC	blood vessel
45	chr3:136298600-136315000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:136298600-136315000	Weak transcription	Small Intestine	intestine
47	chr3:136298600-136351600	Weak transcription	HSMM	muscle
48	chr3:136300000-136335400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:136300200-136351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:136303800-136314000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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