Variant report

Variant	rs3774745
Chromosome Location	chr3:50204745-50204746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50203273..50206743-chr3:50207274..50211024,4	MCF-7	breast:
2	chr3:50193953..50196565-chr3:50203868..50206072,2	MCF-7	breast:
3	chr3:50203834..50205571-chr3:50215186..50218073,2	K562	blood:
4	chr3:50200976..50202928-chr3:50203961..50206728,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000001617	Chromatin interaction
ENSG00000207922	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11711407	0.81[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11714286	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11714799	0.89[ASN][1000 genomes]
rs11717349	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13085567	0.88[ASN][1000 genomes]
rs1858828	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs2073726	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2236942	0.81[JPT][hapmap]
rs2236947	0.87[YRI][hapmap]
rs2282749	0.81[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2526383	0.81[ASN][1000 genomes]
rs34877766	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3755831	0.83[ASN][1000 genomes]
rs3774749	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3774750	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3774751	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688745	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs67627084	0.92[ASN][1000 genomes]
rs9858059	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
7	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
10	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
13	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
15	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
16	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
17	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
20	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
22	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
24	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
25	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
26	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
27	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
28	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3774745	RBM6	cis	lung	GTEx
rs3774745	RBM6	cis	lymphoblastoid	seeQTL
rs3774745	RNF123	cis	cerebellum	SCAN
rs3774745	C3orf62	cis	cerebellum	SCAN
rs3774745	RBM6	cis	Esophagus Muscularis	GTEx
rs3774745	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs3774745	RBM6	cis	Artery Tibial	GTEx
rs3774745	RBM6	cis	cerebellum	SCAN
rs3774745	RBM6	cis	Heart Left Ventricle	GTEx
rs3774745	RBM6	cis	Whole Blood	GTEx
rs3774745	RBM6	cis	Stomach	GTEx
rs3774745	RBM6	cis	Thyroid	GTEx
rs3774745	RNF123	cis	parietal	SCAN
rs3774745	RBM6	cis	parietal	SCAN
rs3774745	PTH1R	cis	parietal	SCAN
rs3774745	RBM6	cis	Nerve Tibial	GTEx
rs3774745	RBM6	cis	Artery Aorta	GTEx
rs3774745	PRSS45	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50194200-50208800	Weak transcription	Pancreas	Pancrea
2	chr3:50194800-50207600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
3	chr3:50195400-50210200	Genic enhancers	Fetal Stomach	stomach
4	chr3:50195400-50210600	Enhancers	Left Ventricle	heart
5	chr3:50195400-50210800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:50196200-50211600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr3:50197200-50211600	Genic enhancers	Esophagus	oesophagus
8	chr3:50197800-50205800	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr3:50197800-50207600	Enhancers	Colonic Mucosa	Colon
10	chr3:50198600-50206400	Enhancers	Gastric	stomach
11	chr3:50199200-50205200	Enhancers	Stomach Mucosa	stomach
12	chr3:50199200-50209400	Enhancers	Placenta	Placenta
13	chr3:50199400-50204800	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr3:50199400-50206400	Enhancers	NHLF	lung
15	chr3:50199800-50204800	Enhancers	Liver	Liver
16	chr3:50200000-50206600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr3:50200000-50209600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:50200000-50210400	Enhancers	Fetal Brain Male	brain
19	chr3:50200200-50205800	Enhancers	Fetal Kidney	kidney
20	chr3:50200400-50204800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:50200600-50206000	Enhancers	Fetal Intestine Large	intestine
22	chr3:50200600-50211800	Enhancers	Right Ventricle	heart
23	chr3:50200800-50204800	Enhancers	Brain Angular Gyrus	brain
24	chr3:50200800-50204800	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr3:50200800-50205600	Enhancers	Fetal Muscle Trunk	muscle
26	chr3:50200800-50205600	Enhancers	HSMMtube	muscle
27	chr3:50201000-50204800	Enhancers	Psoas Muscle	Psoas
28	chr3:50201000-50205000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:50201200-50204800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:50201200-50205000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:50201200-50205400	Enhancers	Brain Cingulate Gyrus	brain
32	chr3:50201200-50206200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:50201200-50206600	Enhancers	Ovary	ovary
34	chr3:50201400-50204800	Enhancers	Fetal Thymus	thymus
35	chr3:50201800-50207400	Enhancers	Brain Hippocampus Middle	brain
36	chr3:50202000-50205400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:50202000-50205400	Enhancers	HSMM	muscle
38	chr3:50202000-50205400	Enhancers	NH-A	brain
39	chr3:50202000-50207200	Enhancers	Small Intestine	intestine
40	chr3:50202000-50210600	Enhancers	A549	lung
41	chr3:50202200-50205800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:50202200-50206200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:50202200-50210400	Enhancers	Lung	lung
44	chr3:50202400-50205800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:50202400-50206400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:50202400-50208800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:50202600-50205400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:50202800-50204800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr3:50202800-50205000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:50202800-50205600	Enhancers	HUES48 Cell Line	embryonic stem cell

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