Variant report

Variant	rs10953329
Chromosome Location	chr7:100865847-100865848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100859700..100862927-chr7:100863052..100866687,4	MCF-7	breast:
2	chr7:100864675..100866290-chr7:100886676..100889459,3	MCF-7	breast:
3	chr7:100863090..100866963-chr7:100885534..100889185,4	MCF-7	breast:
4	chr7:100864193..100867092-chr7:100868840..100870862,2	K562	blood:
5	chr7:100864826..100866353-chr7:100873456..100875578,2	MCF-7	breast:
6	chr7:100864237..100866284-chr7:100885658..100887692,2	K562	blood:
7	chr7:100860186..100862563-chr7:100864132..100865896,2	K562	blood:
8	chr7:100864474..100866546-chr7:100882823..100885224,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000106397	Chromatin interaction
ENSG00000214253	Chromatin interaction
ENSG00000106400	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10250685	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11769624	0.82[MEX][hapmap]
rs17319250	0.83[MEX][hapmap]
rs2072168	0.88[MEX][hapmap]
rs2074685	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302428	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28361887	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35094522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35550811	0.85[EUR][1000 genomes]
rs3757459	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3757460	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3757462	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3807511	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4379383	0.95[LWK][hapmap];0.94[MKK][hapmap]
rs4574779	0.93[LWK][hapmap];0.82[MKK][hapmap]
rs4729670	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs4729672	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4729673	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs7784229	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	63 gene(s)	inside rSNPs	diseases
5	nsv1018841	chr7:100760410-100868299	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv534186	chr7:100773842-100898909	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv607973	chr7:100782460-100873835	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv464651	chr7:100792810-100971604	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv607974	chr7:100792810-100971604	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv429788	chr7:100799565-101178565	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers 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	54 gene(s)	inside rSNPs	diseases
11	esv2752134	chr7:100800131-101141867	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv607975	chr7:100804140-100873835	Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv464652	chr7:100804140-100881640	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv607976	chr7:100804140-100881640	Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv888817	chr7:100804140-100881640	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv607977	chr7:100818846-100881640	Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv831076	chr7:100828847-101011674	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv888818	chr7:100833153-100895480	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
19	nsv888819	chr7:100833153-100920007	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
20	esv2422326	chr7:100833449-101000131	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
21	nsv607978	chr7:100861213-100971604	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10953329	CLDN15	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100862200-100866800	Weak transcription	Small Intestine	intestine
2	chr7:100862200-100875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:100862400-100866000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:100862400-100866000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:100862400-100866000	Weak transcription	Fetal Lung	lung
6	chr7:100862400-100866000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:100862400-100866800	Weak transcription	NHDF-Ad	bronchial
8	chr7:100862400-100867000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:100862400-100867000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:100862400-100867200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:100862400-100867800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:100862400-100868200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:100862400-100874400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:100862400-100875400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:100862400-100887000	Weak transcription	Fetal Kidney	kidney
16	chr7:100862600-100866000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:100862600-100866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:100862600-100866000	Weak transcription	Brain Substantia Nigra	brain
19	chr7:100862600-100866200	Weak transcription	Osteobl	bone
20	chr7:100862600-100866600	Weak transcription	Primary B cells from cord blood	blood
21	chr7:100862600-100866800	Weak transcription	Aorta	Aorta
22	chr7:100862600-100866800	Weak transcription	HSMMtube	muscle
23	chr7:100862600-100868000	Weak transcription	HSMM	muscle
24	chr7:100862800-100866000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:100862800-100875400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:100863200-100867400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr7:100863200-100870200	Weak transcription	Fetal Brain Male	brain
28	chr7:100863200-100872600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:100863200-100874800	Weak transcription	HUVEC	blood vessel
30	chr7:100863200-100875000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr7:100863400-100866000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:100863400-100866600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:100863400-100866800	Weak transcription	HMEC	breast
34	chr7:100863400-100868000	Weak transcription	NH-A	brain
35	chr7:100863600-100866000	Weak transcription	Left Ventricle	heart
36	chr7:100863800-100866000	Weak transcription	Ovary	ovary
37	chr7:100863800-100866000	Weak transcription	GM12878-XiMat	blood
38	chr7:100863800-100872800	Strong transcription	Placenta	Placenta
39	chr7:100863800-100875600	Weak transcription	Right Atrium	heart
40	chr7:100863800-100884000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr7:100863800-100886800	Weak transcription	Psoas Muscle	Psoas
42	chr7:100863800-100886800	Weak transcription	Hela-S3	cervix
43	chr7:100864000-100866000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr7:100864000-100868000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr7:100864000-100873800	Weak transcription	Stomach Mucosa	stomach
46	chr7:100864200-100872800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr7:100864200-100875000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:100864400-100867800	Weak transcription	HepG2	liver
49	chr7:100864400-100871200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr7:100864400-100872600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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