Variant report

Variant	rs200868
Chromosome Location	chr6:5145581-5145582
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	chr6:5145534..5146304-chr8:93741632..93742260,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1571564	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs175596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200860	0.92[ASN][1000 genomes]
rs200862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200865	0.92[EUR][1000 genomes]
rs200866	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs200867	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200869	0.92[ASN][1000 genomes]
rs200870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143693	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2746239	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs373696	0.81[CHD][hapmap]
rs388597	0.86[CHB][hapmap]
rs393055	0.80[ASN][1000 genomes]
rs393300	0.81[CHD][hapmap]
rs393332	0.81[CHD][hapmap]
rs394252	0.90[CHD][hapmap]
rs399120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414986	0.88[ASN][1000 genomes]
rs424006	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs439911	0.81[CHD][hapmap]
rs441463	0.90[CHD][hapmap]
rs450176	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs450649	0.82[AMR][1000 genomes]
rs453113	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs453331	0.81[CHD][hapmap]
rs458108	0.81[CHD][hapmap]
rs458283	0.80[ASN][1000 genomes]
rs458743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs460416	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs460440	0.87[CEU][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs461465	0.80[ASN][1000 genomes]
rs462327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs462487	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs465481	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs466285	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs466369	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4960069	1.00[JPT][hapmap]
rs52401	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591481	0.90[CHD][hapmap]
rs606033	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6597117	1.00[JPT][hapmap]
rs7752848	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7766717	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv5179	chr6:5121824-5167027	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
14	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
15	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
16	nsv1022336	chr6:5145194-5200687	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1018984	chr6:5145194-5200801	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs200868	TUBB2B	cis	cerebellum	SCAN
rs200868	LYRM4	cis	parietal	SCAN
rs200868	LYRM4	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5129000-5162000	Weak transcription	K562	blood
2	chr6:5130600-5172200	Weak transcription	Lung	lung
3	chr6:5133400-5146000	Weak transcription	Psoas Muscle	Psoas
4	chr6:5133400-5151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
6	chr6:5135000-5151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:5135200-5151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:5136400-5151000	Weak transcription	NHEK	skin
9	chr6:5136400-5151600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:5137000-5166600	Weak transcription	Primary T cells from cord blood	blood
11	chr6:5140000-5148600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:5141000-5149200	Weak transcription	Primary B cells from cord blood	blood
13	chr6:5143400-5146200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:5143600-5152400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:5143600-5172400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:5144000-5152400	Weak transcription	Spleen	Spleen
17	chr6:5144000-5152800	Weak transcription	Left Ventricle	heart
18	chr6:5144000-5175400	Weak transcription	HepG2	liver
19	chr6:5144400-5146000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:5144400-5146400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:5144400-5147000	Weak transcription	Fetal Kidney	kidney
22	chr6:5144400-5151800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:5144400-5152800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:5144400-5157200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:5144600-5146000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:5144600-5146200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:5144600-5152400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:5145000-5145600	Strong transcription	Fetal Stomach	stomach
29	chr6:5145000-5146400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:5145000-5147000	Enhancers	Fetal Muscle Trunk	muscle
31	chr6:5145000-5147000	Enhancers	Fetal Muscle Leg	muscle
32	chr6:5145400-5180800	Weak transcription	Fetal Intestine Small	intestine

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