Variant report

Variant	rs2605629
Chromosome Location	chr11:93264037-93264038
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr11:93263019-93264116	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:93256846..93259343-chr11:93261721..93264520,2	K562	blood:
2	chr11:93263943..93267272-chr11:93267950..93271031,3	K562	blood:
3	chr11:93262595..93264552-chr11:93264868..93267737,2	K562	blood:

Variant related genes	Relation type
ENSG00000234106	TF binding region
ENSG00000234106	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10466368	0.82[AMR][1000 genomes]
rs11604909	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs1563445	0.91[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243410	0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248020	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs2248524	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs2248531	0.91[EUR][1000 genomes]
rs2248655	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2263368	0.92[CHB][hapmap]
rs2605611	0.81[ASW][hapmap];0.81[CEU][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs2605614	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2605615	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2605617	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2605620	0.91[EUR][1000 genomes]
rs2605622	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2605623	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2605626	0.91[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2605627	0.88[CEU][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2605628	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2658766	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2658768	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2658769	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2658770	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7116173	0.81[AMR][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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2605629	CCDC67	cis	Thyroid	GTEx
rs2605629	CHORDC1	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93252000-93266800	Enhancers	Fetal Thymus	thymus
2	chr11:93253800-93266200	Weak transcription	Fetal Brain Female	brain
3	chr11:93255000-93274600	Weak transcription	Hela-S3	cervix
4	chr11:93256200-93266000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr11:93256400-93266600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:93257200-93264800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:93257400-93264800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr11:93257400-93266600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr11:93257600-93264400	Enhancers	Fetal Muscle Leg	muscle
10	chr11:93257800-93264200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:93257800-93264200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:93258000-93264600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr11:93258200-93266400	Enhancers	Primary T cells from cord blood	blood
14	chr11:93258400-93274800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:93260400-93266600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:93261400-93264200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr11:93261600-93264200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:93261600-93264200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr11:93261600-93264400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:93261600-93264600	Enhancers	Gastric	stomach
21	chr11:93261600-93264600	Enhancers	Left Ventricle	heart
22	chr11:93261600-93264600	Enhancers	Pancreas	Pancrea
23	chr11:93261600-93264600	Enhancers	Stomach Mucosa	stomach
24	chr11:93262400-93264200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr11:93262400-93264200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr11:93262400-93264600	Enhancers	H9 Cell Line	embryonic stem cell
27	chr11:93262400-93269600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:93262400-93271000	Weak transcription	Aorta	Aorta
29	chr11:93262600-93264200	Enhancers	Fetal Intestine Large	intestine
30	chr11:93262600-93264400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:93262600-93265800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:93262600-93265800	Enhancers	Dnd41	blood
33	chr11:93262800-93266000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr11:93263000-93264200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:93263000-93264600	Enhancers	Fetal Intestine Small	intestine
36	chr11:93263000-93264600	Flanking Active TSS	HepG2	liver
37	chr11:93263000-93264800	Enhancers	Thymus	Thymus
38	chr11:93263000-93266200	Weak transcription	Fetal Stomach	stomach
39	chr11:93263000-93270600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:93263200-93264200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:93263200-93264600	Flanking Active TSS	GM12878-XiMat	blood
42	chr11:93263200-93269400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:93263200-93275200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:93263400-93267800	Weak transcription	Fetal Brain Male	brain
45	chr11:93263400-93268600	Weak transcription	HUVEC	blood vessel
46	chr11:93263400-93269200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr11:93263400-93269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:93263400-93269600	Enhancers	Liver	Liver
49	chr11:93263600-93264600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:93263600-93264600	Weak transcription	Brain Inferior Temporal Lobe	brain

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