Variant report

Variant	rs2395402
Chromosome Location	chr6:33753673-33753674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr6:33753489-33757327	IMR90	lung:	n/a	n/a
2	FOSL2	chr6:33753373-33753971	SK-N-SH	brain:	n/a	chr6:33753747-33753756
3	POLR2A	chr6:33753528-33753879	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr6:33753458-33754807	HUVEC	blood vessel:	n/a	n/a
5	SPI1	chr6:33753280-33753712	HL-60	blood:	n/a	chr6:33753499-33753506
6	POLR2A	chr6:33753584-33753919	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr6:33753568-33753904	HUVEC	blood vessel:	n/a	n/a
8	GATA3	chr6:33753427-33753887	SK-N-SH	brain:	n/a	chr6:33753430-33753440
9	POLR2A	chr6:33753491-33754079	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
2	chr6:33743776..33747465-chr6:33751783..33755243,5	MCF-7	breast:
3	chr6:33752857..33754428-chr6:33763521..33765942,2	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000161904	Chromatin interaction
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12173787	0.89[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12190029	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1359781	0.84[YRI][hapmap];0.90[AFR][1000 genomes]
rs2281820	0.80[CHD][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2296743	0.81[ASW][hapmap]
rs2296744	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2296746	0.92[AFR][1000 genomes]
rs2296747	0.80[AFR][1000 genomes]
rs2296748	0.96[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs3806108	0.81[ASW][hapmap]
rs3806109	0.81[ASW][hapmap]
rs3806110	0.81[ASW][hapmap]
rs4711347	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711348	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711349	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711355	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713678	0.81[EUR][1000 genomes]
rs4713679	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713681	0.80[AFR][1000 genomes]
rs4713682	0.89[AFR][1000 genomes]
rs6457741	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922275	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747694	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751726	0.87[AFR][1000 genomes]
rs7774620	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357164	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394166	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9394167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943478	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS 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	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2395402	LEMD2	cis	cerebellum	SCAN
rs2395402	LEMD2	cis	parietal	SCAN
rs2395402	PSMB9	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:33740200-33754000	Strong transcription	Primary B cells from cord blood	blood
3	chr6:33740600-33754200	Strong transcription	Fetal Intestine Large	intestine
4	chr6:33740600-33754200	Strong transcription	Fetal Intestine Small	intestine
5	chr6:33741000-33754000	Strong transcription	Fetal Thymus	thymus
6	chr6:33744200-33754400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:33746600-33755000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:33748000-33754200	Weak transcription	Psoas Muscle	Psoas
9	chr6:33750400-33753800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:33750400-33754000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:33750400-33755000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:33751000-33754000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:33751600-33754400	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr6:33751600-33755200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:33751800-33754600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:33752000-33754400	Genic enhancers	Left Ventricle	heart
17	chr6:33752000-33754600	Genic enhancers	Adipose Nuclei	Adipose
18	chr6:33752000-33754600	Weak transcription	Fetal Brain Male	brain
19	chr6:33752000-33755000	Genic enhancers	Brain Cingulate Gyrus	brain
20	chr6:33752200-33753800	Weak transcription	K562	blood
21	chr6:33752400-33753800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:33752400-33753800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
23	chr6:33752400-33754200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:33752400-33754400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:33752400-33754400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr6:33752400-33754400	Genic enhancers	Pancreas	Pancrea
27	chr6:33752400-33754400	Genic enhancers	Rectal Smooth Muscle	rectum
28	chr6:33752400-33754600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr6:33752400-33754800	Genic enhancers	Stomach Smooth Muscle	stomach
30	chr6:33752600-33753800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:33752600-33753800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:33752600-33754000	Genic enhancers	H1 Cell Line	embryonic stem cell
33	chr6:33752600-33754000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:33752600-33754200	Genic enhancers	Duodenum Mucosa	Duodenum
35	chr6:33752600-33754400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:33752600-33754400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:33752600-33754400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:33752600-33754600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr6:33752600-33754600	Genic enhancers	Colon Smooth Muscle	Colon
40	chr6:33752600-33755000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:33752600-33755200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:33752600-33755600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:33752800-33754000	Genic enhancers	Brain Germinal Matrix	brain
44	chr6:33752800-33754200	Genic enhancers	Dnd41	blood
45	chr6:33752800-33754400	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr6:33752800-33754800	Genic enhancers	Osteobl	bone
47	chr6:33752800-33755200	Genic enhancers	Brain Hippocampus Middle	brain
48	chr6:33752800-33755400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:33752800-33755400	Genic enhancers	Fetal Muscle Leg	muscle
50	chr6:33752800-33755400	Genic enhancers	Placenta	Placenta

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