Variant report

Variant	rs2878
Chromosome Location	chr7:102953621-102953622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:102953286..102955465-chr7:102961116..102963832,3	MCF-7	breast:
2	chr7:102951762..102954038-chr7:102964759..102967484,2	K562	blood:
3	chr7:102952502..102955468-chr7:102982681..102986530,4	K562	blood:
4	chr7:102714837..102716641-chr7:102952757..102955113,2	MCF-7	breast:
5	chr7:102951782..102954564-chr7:102958545..102960643,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161040	Chromatin interaction
ENSG00000170632	Chromatin interaction
ENSG00000105821	Chromatin interaction
ENSG00000161057	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10245155	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10257369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs10266523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10268808	0.87[CEU][hapmap]
rs10271758	0.85[EUR][1000 genomes]
rs10486853	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs11978339	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17136078	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs17136079	0.93[CEU][hapmap]
rs17136083	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs17136728	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17606134	0.82[JPT][hapmap]
rs17680523	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17837510	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs1861731	0.93[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs1968201	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs2193420	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs3087615	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35399723	0.93[ASN][1000 genomes]
rs4266582	0.93[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4593456	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4727563	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs4727566	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs4727568	0.80[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4729887	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4729891	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs4729896	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4729899	0.93[CEU][hapmap]
rs4729902	0.93[CEU][hapmap]
rs4729911	0.93[ASN][1000 genomes]
rs5025411	0.84[GIH][hapmap];0.82[JPT][hapmap]
rs62481648	0.83[EUR][1000 genomes]
rs62481654	0.81[EUR][1000 genomes]
rs62481655	0.89[EUR][1000 genomes]
rs62482371	0.89[EUR][1000 genomes]
rs62482394	0.97[ASN][1000 genomes]
rs62482396	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482397	0.97[ASN][1000 genomes]
rs62482398	0.97[ASN][1000 genomes]
rs62482399	0.97[ASN][1000 genomes]
rs62482403	0.97[ASN][1000 genomes]
rs6971734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6972190	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73175837	0.97[ASN][1000 genomes]
rs7455141	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs7777392	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7804020	0.82[JPT][hapmap]
rs7810558	0.89[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	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv831084	chr7:102778908-102964970	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2878	MCAT	trans	brain	seeQTL
rs2878	ZNF789	cis	cerebellum	SCAN
rs2878	DNAJC2	cis	parietal	SCAN
rs2878	HTRA2	trans	brain	seeQTL
rs2878	RP11-401L13.5	cis	Thyroid	GTEx
rs2878	PSMC2	cis	parietal	SCAN
rs2878	ZNF655	cis	parietal	SCAN
rs2878	MRPL55	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102938400-102957000	Weak transcription	Spleen	Spleen
2	chr7:102938600-102957000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:102938600-102984200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:102938800-102957000	Weak transcription	Aorta	Aorta
5	chr7:102939000-102965200	Weak transcription	Right Ventricle	heart
6	chr7:102939000-102969200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr7:102939200-102962000	Weak transcription	Right Atrium	heart
8	chr7:102939200-102967400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr7:102939200-102968400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr7:102939200-102968400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:102939200-102972400	Strong transcription	Fetal Thymus	thymus
12	chr7:102939400-102958800	Weak transcription	Gastric	stomach
13	chr7:102939400-102964800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:102939400-102965600	Strong transcription	Fetal Lung	lung
15	chr7:102939400-102966800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:102939400-102967800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:102939400-102967800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:102939400-102968000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:102939400-102968000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr7:102939400-102968200	Strong transcription	Placenta	Placenta
21	chr7:102939400-102968200	Strong transcription	HSMM	muscle
22	chr7:102939400-102969800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:102939600-102963200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr7:102939600-102965400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr7:102939600-102966800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr7:102939600-102968000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:102939600-102968000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr7:102939600-102968000	Strong transcription	Fetal Intestine Large	intestine
29	chr7:102939600-102968000	Strong transcription	Fetal Muscle Leg	muscle
30	chr7:102939600-102968400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:102939600-102968400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:102939600-102968600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:102939600-102969800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:102939600-102970000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:102939800-102959600	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr7:102939800-102960600	Strong transcription	NH-A	brain
37	chr7:102939800-102960800	Strong transcription	Brain Germinal Matrix	brain
38	chr7:102939800-102962400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:102939800-102968000	Strong transcription	Adipose Nuclei	Adipose
40	chr7:102939800-102968000	Strong transcription	Osteobl	bone
41	chr7:102939800-102968200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:102939800-102968200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr7:102939800-102968200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr7:102939800-102969800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:102939800-102980800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:102939800-102984000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr7:102939800-102984200	Weak transcription	Stomach Mucosa	stomach
48	chr7:102940000-102956800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:102940000-102960400	Strong transcription	Primary B cells from cord blood	blood
50	chr7:102940000-102961600	Strong transcription	Brain Anterior Caudate	brain

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