Variant report

Variant	rs938554
Chromosome Location	chr4:9925692-9925693
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:9924672..9926796-chr4:10008145..10009788,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DRD5-1	chr4:9925400-9925770	ENSG00000249219.1

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10010582	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10017945	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10516194	1.00[CHB][hapmap]
rs1071988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10939637	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10939638	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11722229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11723439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11726102	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11727666	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11734219	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11735831	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11942223	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12498742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12507606	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12509955	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13102218	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13106991	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13111638	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13115469	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13125209	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13125646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs13131257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13137069	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13145758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16868246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16890979	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235345	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4385059	1.00[JPT][hapmap]
rs4475146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4481233	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4637402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4639073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4697699	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4697700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4697913	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5028843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6449173	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6449213	1.00[JPT][hapmap]
rs6823324	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6827401	1.00[CHB][hapmap]
rs6828184	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6832439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6832456	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6837336	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6838021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6855911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6856396	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs734553	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs737267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7376960	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7377625	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7439210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7442295	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7669607	1.00[CHB][hapmap]
rs7670751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7680126	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7682751	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs874432	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9291642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs938552	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs938555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs938564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9991278	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9998811	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
2	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	nsv1014216	chr4:9713612-10223836	Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
4	nsv1010249	chr4:9716101-10086188	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv878672	chr4:9786732-10008305	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv878676	chr4:9797703-9978094	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv878677	chr4:9797703-10008305	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1007593	chr4:9802146-9956285	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878681	chr4:9802853-10397327	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
10	nsv997941	chr4:9805223-10493388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
11	nsv1008649	chr4:9805223-10589802	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
12	nsv1000587	chr4:9805223-10610752	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
13	nsv537022	chr4:9805223-10610752	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
14	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
15	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
16	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
17	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
18	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription 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	58 gene(s)	inside rSNPs	diseases
19	nsv1004311	chr4:9825814-9978414	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv998425	chr4:9834666-9961280	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	esv2763339	chr4:9858426-10056376	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv878684	chr4:9863698-9998440	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv878686	chr4:9893403-10008305	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv537026	chr4:9903566-10262258	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
25	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
26	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
27	esv2752052	chr4:9911872-10313111	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
28	nsv527211	chr4:9912101-9944650	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv878687	chr4:9912101-10008305	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	nsv878688	chr4:9915850-10038112	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:9903600-9928600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr4:9903600-9929000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr4:9908000-9943000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:9911400-9979800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:9914200-9926000	Weak transcription	Spleen	Spleen
6	chr4:9915400-9928000	Strong transcription	Fetal Intestine Small	intestine
7	chr4:9918600-9948600	Weak transcription	Pancreas	Pancrea
8	chr4:9920200-9943400	Weak transcription	Aorta	Aorta
9	chr4:9920400-9926400	Weak transcription	Right Ventricle	heart
10	chr4:9921400-9926000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:9921600-9926400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:9921600-9929000	Weak transcription	Left Ventricle	heart
13	chr4:9921600-9941000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:9922800-9925800	Weak transcription	NHEK	skin
15	chr4:9922800-9926200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:9922800-9928200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:9922800-9931200	Weak transcription	Liver	Liver
18	chr4:9923200-9926400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:9923200-9927800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:9923200-9932800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:9924200-9925800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:9924400-9927200	Enhancers	Fetal Muscle Trunk	muscle
23	chr4:9924600-9928000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:9924600-9928000	Enhancers	HMEC	breast
25	chr4:9924800-9925800	Strong transcription	HepG2	liver
26	chr4:9924800-9926400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:9925200-9927200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr4:9925200-9927200	Enhancers	Fetal Muscle Leg	muscle
29	chr4:9925400-9925800	Weak transcription	Esophagus	oesophagus
30	chr4:9925400-9925800	Enhancers	Stomach Mucosa	stomach
31	chr4:9925400-9931000	Weak transcription	Fetal Intestine Large	intestine

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