Variant report

Variant	rs11680950
Chromosome Location	chr2:96844981-96844982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96844974..96848184-chr2:96864980..96867697,3	K562	blood:
2	chr2:96837701..96840324-chr2:96842063..96845006,2	K562	blood:
3	chr2:96844014..96846474-chr2:96864847..96866612,2	K562	blood:
4	chr2:96838596..96845303-chr2:96871410..96876141,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STARD7-1	chr2:96844414-96845254	l_1892_chr2:96841666-96845254_testes

Variant related genes	Relation type
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10183151	0.90[CEU][hapmap];0.80[YRI][hapmap]
rs11687113	0.82[GIH][hapmap]
rs1168965	0.90[CEU][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap]
rs1168966	0.81[CEU][hapmap]
rs1168968	0.95[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs1168970	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1168974	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1168975	0.95[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs1168976	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1657502	0.81[CEU][hapmap]
rs2229169	0.90[CEU][hapmap];0.89[JPT][hapmap]
rs2301707	0.95[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs2312955	0.85[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap]
rs2438978	0.80[YRI][hapmap]
rs2462774	0.87[YRI][hapmap]
rs2692893	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap]
rs2692894	0.90[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap]
rs2969490	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs2969491	0.90[CEU][hapmap];0.84[JPT][hapmap]
rs3821051	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4144055	0.82[GIH][hapmap];0.88[YRI][hapmap]
rs4426564	0.95[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap]
rs4907299	0.85[CEU][hapmap]
rs6740563	0.89[YRI][hapmap]
rs749459	0.81[CEU][hapmap]
rs7604842	0.89[CEU][hapmap]
rs772175	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs772178	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs810057	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs893173	0.83[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3435047	chr2:96836850-96890437	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11680950	MGAT4A	cis	parietal	SCAN
rs11680950	MRPL30	cis	parietal	SCAN
rs11680950	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96828200-96850000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:96830600-96850000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:96837800-96849800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:96838000-96850200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:96840400-96845600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:96840400-96845800	Weak transcription	Primary T cells from cord blood	blood
7	chr2:96840400-96845800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:96840400-96845800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:96840400-96848600	Weak transcription	Thymus	Thymus
10	chr2:96840400-96849200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:96840400-96849400	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:96840400-96849400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:96840400-96849600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:96840400-96849800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:96840400-96850000	Weak transcription	Primary B cells from cord blood	blood
16	chr2:96840400-96850000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:96840400-96850000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:96840400-96850000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:96840400-96850000	Weak transcription	Pancreas	Pancrea
20	chr2:96840400-96850000	Weak transcription	Spleen	Spleen
21	chr2:96840400-96850200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:96840400-96850400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:96840400-96850600	Weak transcription	K562	blood
24	chr2:96840400-96851200	Weak transcription	Hela-S3	cervix
25	chr2:96840400-96851600	Weak transcription	Colonic Mucosa	Colon
26	chr2:96840600-96845800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:96840600-96846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr2:96840600-96849800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:96840800-96850400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:96842000-96849200	Weak transcription	Left Ventricle	heart
31	chr2:96842000-96849800	Weak transcription	Brain Anterior Caudate	brain
32	chr2:96842200-96849000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:96842200-96849600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:96842200-96849800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:96842200-96850000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:96842200-96850000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:96842400-96849600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:96842400-96850000	Weak transcription	HSMMtube	muscle
39	chr2:96842600-96848600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:96842600-96849200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:96842600-96850000	Weak transcription	Right Ventricle	heart
42	chr2:96842600-96850000	Weak transcription	HSMM	muscle
43	chr2:96842600-96850000	Weak transcription	NHLF	lung
44	chr2:96842600-96850400	Weak transcription	NH-A	brain
45	chr2:96842600-96850800	Weak transcription	NHDF-Ad	bronchial
46	chr2:96842600-96861600	Weak transcription	Right Atrium	heart
47	chr2:96842800-96849000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:96842800-96849000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:96842800-96849600	Weak transcription	Osteobl	bone
50	chr2:96843400-96850600	Weak transcription	Fetal Heart	heart

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