Variant report

Variant	rs12190412
Chromosome Location	chr6:5203952-5203953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5200460..5201968-chr6:5202592..5204399,2	MCF-7	breast:
2	chr6:5203877..5206736-chr6:5207600..5210343,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10458084	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10458086	0.83[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10498665	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11242995	0.91[JPT][hapmap]
rs12204340	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12209713	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12215806	0.83[ASN][1000 genomes]
rs12660749	0.92[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2143692	0.81[JPT][hapmap]
rs41302851	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4144009	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs4959333	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4959336	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4960072	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6901828	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6934882	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7739582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7740952	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7763280	0.83[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7764853	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9791263	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
11	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12190412	MGC39372	cis	cerebellum	SCAN
rs12190412	LYRM4	cis	Thyroid	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5176200-5239600	Weak transcription	Thymus	Thymus
2	chr6:5177800-5205200	Weak transcription	Aorta	Aorta
3	chr6:5179200-5207600	Weak transcription	Primary B cells from cord blood	blood
4	chr6:5180200-5212200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:5180600-5205000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:5180600-5205800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:5180600-5208200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:5181200-5204600	Weak transcription	Esophagus	oesophagus
9	chr6:5182000-5213600	Weak transcription	Gastric	stomach
10	chr6:5186400-5205000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:5189000-5213200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:5189400-5205400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:5191000-5206600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:5191600-5204600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:5191800-5204800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:5191800-5204800	Weak transcription	HSMM	muscle
17	chr6:5191800-5206000	Weak transcription	NHLF	lung
18	chr6:5191800-5206400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:5192000-5205800	Weak transcription	A549	lung
20	chr6:5192800-5213000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:5193000-5204200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:5193000-5205200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:5193200-5204600	Weak transcription	Lung	lung
24	chr6:5193200-5212400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:5193400-5204200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:5193400-5204200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:5193400-5204600	Weak transcription	Brain Angular Gyrus	brain
28	chr6:5193400-5205000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:5194000-5220800	Weak transcription	GM12878-XiMat	blood
30	chr6:5195000-5205000	Weak transcription	Fetal Intestine Large	intestine
31	chr6:5195800-5207800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr6:5196600-5204600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:5196800-5204000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:5196800-5205000	Weak transcription	Pancreas	Pancrea
35	chr6:5197000-5206000	Weak transcription	K562	blood
36	chr6:5197200-5205200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:5198200-5204800	Weak transcription	Liver	Liver
38	chr6:5199800-5206200	Enhancers	Fetal Heart	heart
39	chr6:5199800-5207800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr6:5200200-5206200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:5201000-5204200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:5201200-5204000	Weak transcription	Ovary	ovary
43	chr6:5201200-5204800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:5201200-5208800	Enhancers	Fetal Muscle Leg	muscle
45	chr6:5201400-5205600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:5201600-5213400	Weak transcription	Fetal Brain Male	brain
47	chr6:5201800-5204000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:5201800-5204000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:5201800-5204400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:5201800-5205000	Weak transcription	Muscle Satellite Cultured Cells	--

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