Variant report

Variant	rs353631
Chromosome Location	chr11:35187568-35187569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:35186531..35188215-chr11:35413426..35415708,2	MCF-7	breast:
2	chr11:35160960..35162794-chr11:35186248..35188654,2	MCF-7	breast:
3	chr11:35187046..35189640-chr11:35384110..35385949,2	MCF-7	breast:
4	chr11:35186608..35189447-chr11:35199235..35201624,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs102518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193276	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353612	0.82[ASW][hapmap];0.84[CEU][hapmap];0.92[LWK][hapmap];0.83[MKK][hapmap];0.83[AFR][1000 genomes]
rs353628	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs353629	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs353632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353637	0.85[MKK][hapmap]
rs353638	0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353643	0.89[CEU][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2758263	chr11:35029933-35226784	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2759818	chr11:35029933-35238578	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv541001	chr11:35053717-35224624	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv2757437	chr11:35067482-35238578	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv2752912	chr11:35074167-35238578	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv508623	chr11:35094933-35203363	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised 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	23 gene(s)	inside rSNPs	diseases
8	nsv541002	chr11:35101282-35224624	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv541003	chr11:35122694-35261451	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3693078	chr11:35179651-35217745	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs353631	RAG1	cis	cerebellum	SCAN
rs353631	TRAF6	cis	parietal	SCAN
rs353631	TCP11L1	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35161200-35197400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
2	chr11:35172200-35196000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:35177600-35191000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:35179600-35188000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:35180600-35187800	Weak transcription	Lung	lung
6	chr11:35180600-35188000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:35180800-35187800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:35180800-35189400	Weak transcription	Fetal Intestine Small	intestine
9	chr11:35181000-35187600	Weak transcription	HSMMtube	muscle
10	chr11:35181400-35187600	Weak transcription	Brain Hippocampus Middle	brain
11	chr11:35181600-35187600	Weak transcription	Brain Substantia Nigra	brain
12	chr11:35182200-35188000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:35182600-35190200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr11:35182800-35188200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:35183000-35188000	Enhancers	Colon Smooth Muscle	Colon
16	chr11:35183200-35188000	Enhancers	Adipose Nuclei	Adipose
17	chr11:35183600-35187600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:35184000-35190200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr11:35184200-35189600	Enhancers	Pancreas	Pancrea
20	chr11:35184400-35188200	Weak transcription	Psoas Muscle	Psoas
21	chr11:35184400-35191000	Enhancers	Fetal Stomach	stomach
22	chr11:35184600-35187600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:35184600-35187600	Weak transcription	Brain Anterior Caudate	brain
24	chr11:35184600-35188000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr11:35185000-35188600	Enhancers	Colonic Mucosa	Colon
26	chr11:35185200-35187600	Genic enhancers	NHEK	skin
27	chr11:35185600-35187600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr11:35185600-35188000	Enhancers	Rectal Smooth Muscle	rectum
29	chr11:35185600-35190600	Enhancers	Small Intestine	intestine
30	chr11:35185600-35194200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:35185800-35189200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:35186000-35187600	Enhancers	NH-A	brain
33	chr11:35186000-35187800	Weak transcription	Aorta	Aorta
34	chr11:35186200-35187600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:35186200-35188200	Enhancers	Fetal Muscle Leg	muscle
36	chr11:35186200-35189400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:35186200-35189600	Enhancers	HUVEC	blood vessel
38	chr11:35186200-35191400	Weak transcription	Fetal Kidney	kidney
39	chr11:35186400-35187600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr11:35186400-35187600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr11:35186400-35187600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:35186400-35187600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr11:35186400-35187600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr11:35186400-35187800	Enhancers	HSMM	muscle
45	chr11:35186400-35188600	Enhancers	Stomach Mucosa	stomach
46	chr11:35186400-35188600	Flanking Active TSS	Dnd41	blood
47	chr11:35186400-35189600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr11:35186400-35189800	Enhancers	Left Ventricle	heart
49	chr11:35186400-35190400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr11:35186600-35187600	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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