Variant report

Variant	rs12421636
Chromosome Location	chr11:36400379-36400380
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	chr11:36400346..36402601-chr11:36405590..36407328,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAG1-4	chr11:36399074-36400759	NONHSAT018823

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10836544	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033602	1.00[YRI][hapmap]
rs11608110	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418784	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12421645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812774	1.00[YRI][hapmap]
rs72950073	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72950076	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72950079	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72950084	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72950090	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36397400-36401000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr11:36397600-36402000	Active TSS	Rectal Smooth Muscle	rectum
3	chr11:36397600-36402200	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr11:36398000-36400600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:36398400-36401200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:36399400-36401000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:36399400-36402200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
8	chr11:36399600-36401600	Active TSS	Colonic Mucosa	Colon
9	chr11:36399800-36400600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:36399800-36400600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:36399800-36400600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:36399800-36400600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr11:36399800-36400600	Active TSS	NH-A	brain
14	chr11:36399800-36400800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:36399800-36400800	Enhancers	Brain Angular Gyrus	brain
16	chr11:36399800-36401400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:36399800-36401600	Weak transcription	Lung	lung
18	chr11:36399800-36401800	Weak transcription	Left Ventricle	heart
19	chr11:36399800-36403200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:36399800-36406800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:36399800-36411800	Weak transcription	HSMM	muscle
22	chr11:36400000-36400400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:36400000-36400400	Enhancers	Colon Smooth Muscle	Colon
24	chr11:36400000-36400400	Active TSS	Fetal Intestine Small	intestine
25	chr11:36400000-36400600	Active TSS	Primary T cells from cord blood	blood
26	chr11:36400000-36400600	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
27	chr11:36400000-36400800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:36400000-36400800	Enhancers	Brain Anterior Caudate	brain
29	chr11:36400000-36400800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr11:36400000-36401200	Active TSS	Primary T cells fromperipheralblood	blood
31	chr11:36400000-36401200	Enhancers	NHEK	skin
32	chr11:36400000-36401400	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr11:36400000-36401400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:36400000-36401800	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr11:36400000-36401800	Weak transcription	Placenta	Placenta
36	chr11:36400000-36402600	Weak transcription	Ovary	ovary
37	chr11:36400000-36402800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:36400000-36402800	Enhancers	Brain Substantia Nigra	brain
39	chr11:36400000-36403400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:36400000-36403600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:36400000-36403800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:36400000-36403800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:36400000-36403800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:36400000-36403800	Weak transcription	Spleen	Spleen
45	chr11:36400000-36403800	Weak transcription	HMEC	breast
46	chr11:36400000-36404200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:36400000-36408000	Weak transcription	Thymus	Thymus
48	chr11:36400000-36409400	Weak transcription	Adipose Nuclei	Adipose
49	chr11:36400000-36409800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:36400000-36412400	Weak transcription	Osteobl	bone

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