Variant report

Variant	rs2271997
Chromosome Location	chr11:18303404-18303405
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	chr11:18302739..18305264-chr11:18414921..18417198,2	MCF-7	breast:
2	chr11:18301994..18303954-chr11:18343927..18346094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110768	Chromatin interaction
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1046611	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024601	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024602	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12218	0.83[CEU][hapmap]
rs3781945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4150667	0.83[JPT][hapmap]
rs7945996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2271997	LDHA	cis	parietal	SCAN
rs2271997	GTF2H1	cis	parietal	SCAN
rs2271997	GTF2H1	cis	cerebellum	SCAN
rs2271997	MRGPRX4	cis	parietal	SCAN
rs2271997	HPS5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18285600-18308400	Weak transcription	Gastric	stomach
2	chr11:18287600-18334000	Weak transcription	Right Atrium	heart
3	chr11:18291800-18307800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:18291800-18314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:18292000-18303600	Weak transcription	Brain Germinal Matrix	brain
6	chr11:18292000-18308400	Weak transcription	Right Ventricle	heart
7	chr11:18292000-18314800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:18293800-18303800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:18293800-18304200	Weak transcription	Brain Substantia Nigra	brain
10	chr11:18293800-18306200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:18295200-18308000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:18295800-18307800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:18296800-18315400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:18297000-18307200	Weak transcription	Fetal Brain Male	brain
15	chr11:18297400-18328400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:18298200-18306600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr11:18298200-18333800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:18298600-18326200	Strong transcription	Liver	Liver
19	chr11:18298800-18314200	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr11:18298800-18327600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:18298800-18331600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:18299000-18306200	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:18299000-18308400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:18299200-18304800	Strong transcription	Primary T cells from cord blood	blood
25	chr11:18299200-18305800	Weak transcription	Fetal Thymus	thymus
26	chr11:18299200-18306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr11:18299200-18322000	Strong transcription	HMEC	breast
28	chr11:18299200-18332400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:18299600-18309600	Strong transcription	NH-A	brain
30	chr11:18299600-18326200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:18299600-18334200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:18299800-18307800	Weak transcription	HUVEC	blood vessel
33	chr11:18300000-18306600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:18300000-18320600	Strong transcription	Left Ventricle	heart
35	chr11:18300000-18328600	Weak transcription	Stomach Mucosa	stomach
36	chr11:18300000-18334400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:18300200-18306800	Strong transcription	Fetal Brain Female	brain
38	chr11:18300200-18307800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr11:18300200-18312000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr11:18300200-18320800	Strong transcription	Fetal Intestine Large	intestine
41	chr11:18300200-18323600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr11:18300200-18333600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:18300200-18334000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:18300200-18334800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:18300200-18336000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:18300600-18304800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:18300600-18323600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:18300600-18331600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:18300600-18332600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:18300600-18333200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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