Variant report

Variant	rs6746234
Chromosome Location	chr2:234433081-234433082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234427830..234430556-chr2:234432658..234434304,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1046976	1.00[CHB][hapmap]
rs10929178	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11675254	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11675858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11676524	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11686188	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11694406	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs3754595	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3796090	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs3796092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3820744	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3828307	1.00[CHB][hapmap]
rs4047189	0.91[ASW][hapmap];0.85[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6704644	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6753242	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs72980395	0.88[EUR][1000 genomes]
rs72980402	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72982309	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72982316	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72982325	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587876	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7598771	0.85[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6746234	ECEL1P2	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
3	chr2:234398000-234452800	Weak transcription	HUVEC	blood vessel
4	chr2:234398400-234442400	Weak transcription	Hela-S3	cervix
5	chr2:234402200-234472400	Weak transcription	Psoas Muscle	Psoas
6	chr2:234402600-234436800	Weak transcription	Gastric	stomach
7	chr2:234402600-234454000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:234404400-234455000	Weak transcription	Fetal Thymus	thymus
9	chr2:234407800-234436800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:234411600-234465600	Weak transcription	Thymus	Thymus
11	chr2:234412400-234437600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:234412600-234437400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:234413000-234474200	Weak transcription	Fetal Heart	heart
14	chr2:234413200-234440600	Weak transcription	Dnd41	blood
15	chr2:234414000-234461800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:234415400-234440600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:234416200-234441200	Weak transcription	Fetal Kidney	kidney
18	chr2:234416200-234441800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:234418600-234436400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:234423200-234473400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:234423600-234439600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:234423800-234441400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:234424600-234433600	Weak transcription	K562	blood
24	chr2:234426200-234474000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:234426400-234453600	Weak transcription	NH-A	brain
26	chr2:234427000-234466200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:234427200-234438200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:234427200-234438200	Strong transcription	Liver	Liver
29	chr2:234427200-234438200	Strong transcription	Placenta	Placenta
30	chr2:234427200-234438400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:234427200-234438400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:234427400-234433200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr2:234427400-234434800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr2:234427400-234435200	Strong transcription	Adipose Nuclei	Adipose
35	chr2:234427400-234438200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:234427400-234440600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:234427400-234463800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:234427600-234440400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:234428600-234433800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:234428600-234440800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:234428600-234440800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:234428800-234474400	Weak transcription	Brain Germinal Matrix	brain
43	chr2:234429000-234433600	Strong transcription	Osteobl	bone
44	chr2:234429600-234438400	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:234429800-234434600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:234429800-234434600	Strong transcription	Brain Substantia Nigra	brain
47	chr2:234429800-234434800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:234429800-234435200	Strong transcription	A549	lung
49	chr2:234429800-234437800	Strong transcription	Left Ventricle	heart
50	chr2:234429800-234438400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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