Variant report

Variant	rs11677050
Chromosome Location	chr2:113328882-113328883
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113327941..113330721-chr2:113336022..113338098,2	K562	blood:
2	chr2:113327443..113331173-chr2:113335823..113339946,4	MCF-7	breast:
3	chr2:113291521..113293955-chr2:113328145..113330168,2	K562	blood:
4	chr2:113317506..113319132-chr2:113326152..113328892,2	K562	blood:
5	chr2:113328823..113332767-chr2:113340329..113343194,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207383	Chromatin interaction
ENSG00000125611	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10153558	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs10153801	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs10864905	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123139	0.92[ASN][1000 genomes]
rs11123140	0.88[ASN][1000 genomes]
rs11123141	0.89[ASN][1000 genomes]
rs11675730	0.92[ASN][1000 genomes]
rs11676962	0.92[ASN][1000 genomes]
rs11689338	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618629	0.94[ASN][1000 genomes]
rs12618882	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13015669	0.92[ASN][1000 genomes]
rs1437673	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1437675	0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1545133	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1595388	0.91[ASN][1000 genomes]
rs2304555	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35832933	0.91[ASN][1000 genomes]
rs3748024	0.89[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3789723	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816140	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3816141	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3961775	0.92[ASN][1000 genomes]
rs41278940	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41280572	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849072	0.92[ASN][1000 genomes]
rs4849073	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4849074	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4849075	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849076	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56081241	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60703755	0.92[ASN][1000 genomes]
rs7568539	0.92[ASN][1000 genomes]
rs7578724	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7607358	1.00[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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11677050	POLR1B	cis	parietal	SCAN
rs11677050	FBLN7	cis	parietal	SCAN
rs11677050	POLR1B	cis	cerebellum	SCAN
rs11677050	LOC653596	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
2	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113303000-113334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:113303000-113334400	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr2:113303000-113335200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:113303200-113334200	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:113303200-113334600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:113303400-113334400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:113303400-113334600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:113303600-113334000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr2:113303600-113334400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:113303600-113334400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr2:113303600-113334400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr2:113303600-113334600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:113303600-113334600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:113303600-113334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:113303600-113334800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:113303600-113335000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:113303600-113335000	Strong transcription	Fetal Thymus	thymus
20	chr2:113303600-113335200	Strong transcription	Fetal Muscle Leg	muscle
21	chr2:113303800-113334800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:113304400-113333600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:113304400-113334200	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr2:113304400-113334400	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:113304400-113335000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:113304600-113329400	Strong transcription	Fetal Stomach	stomach
27	chr2:113304600-113334400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:113305400-113334000	Strong transcription	Adipose Nuclei	Adipose
29	chr2:113305400-113334800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:113306600-113334400	Strong transcription	Liver	Liver
31	chr2:113306800-113334600	Strong transcription	HepG2	liver
32	chr2:113311200-113331200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:113312400-113334400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:113314600-113335000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:113314800-113334600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:113315400-113333800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr2:113315600-113335000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:113317000-113331200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:113320200-113329800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:113320800-113334200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:113320800-113334800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:113320800-113335000	Strong transcription	A549	lung
43	chr2:113321000-113334400	Strong transcription	Fetal Intestine Large	intestine
44	chr2:113321200-113334200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:113321200-113335000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:113321600-113334400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:113321600-113334600	Strong transcription	NHEK	skin
48	chr2:113322200-113334200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:113323800-113333800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:113324600-113334000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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