Variant report

Variant	rs7257310
Chromosome Location	chr19:41827120-41827121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41813982..41818537-chr19:41824784..41829010,7	MCF-7	breast:
2	chr19:41824554..41827469-chr19:41868894..41871689,2	K562	blood:
3	chr19:41826823..41830968-chr19:41831922..41834042,4	K562	blood:
4	chr19:41821189..41824039-chr19:41826906..41830511,3	MCF-7	breast:
5	chr19:41825498..41830119-chr19:41857290..41861615,7	MCF-7	breast:
6	chr19:41825452..41832651-chr19:41855170..41863054,16	K562	blood:

Variant related genes	Relation type
ENSG00000142046	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000123810	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10410836	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10421990	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1056854	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs11466347	0.83[EUR][1000 genomes]
rs11466359	0.98[EUR][1000 genomes]
rs11879562	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880564	0.98[EUR][1000 genomes]
rs11881940	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs11881953	0.82[EUR][1000 genomes]
rs11882467	0.90[CHB][hapmap]
rs12327659	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462203	0.85[CHB][hapmap]
rs12972266	0.92[EUR][1000 genomes]
rs12974323	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974420	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs12975585	0.90[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12975920	0.98[ASN][1000 genomes]
rs12976536	0.86[EUR][1000 genomes]
rs12978323	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12980298	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980480	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12980839	0.95[ASN][1000 genomes]
rs12980942	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12981053	0.86[EUR][1000 genomes]
rs12983047	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984160	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs12985162	0.91[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs12985339	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs13345456	0.99[ASN][1000 genomes]
rs16958994	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958996	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958999	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1865051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1865052	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1865053	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053086	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2241718	1.00[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs2241719	0.98[EUR][1000 genomes]
rs2241720	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2304230	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304234	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs34075897	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34322801	0.93[EUR][1000 genomes]
rs34945449	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35501756	0.95[EUR][1000 genomes]
rs35812313	0.86[EUR][1000 genomes]
rs3745295	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3752705	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816052	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4456618	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802111	0.85[CHB][hapmap]
rs4802112	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4802113	0.84[CHB][hapmap]
rs4803448	0.85[CHB][hapmap]
rs4803449	0.85[CHB][hapmap]
rs6508974	0.85[CHB][hapmap]
rs66724427	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67511749	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67744888	0.86[EUR][1000 genomes]
rs6957	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7245398	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246525	0.85[CHB][hapmap]
rs7248164	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254679	0.82[CEU][hapmap];0.95[ASN][1000 genomes]
rs7256416	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7256856	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257742	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257825	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258749	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103839	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs8105161	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105901	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs8109167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109627	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911769	chr19:41813676-41845801	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7257310	PLEKHA4	cis	cerebellum	SCAN
rs7257310	FLT3LG	cis	cerebellum	SCAN
rs7257310	BAX	cis	cerebellum	SCAN
rs7257310	TSKS	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41817000-41827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41817200-41827200	Weak transcription	Right Atrium	heart
3	chr19:41817600-41827600	Strong transcription	Fetal Stomach	stomach
4	chr19:41817800-41827200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:41817800-41828800	Strong transcription	Fetal Intestine Small	intestine
6	chr19:41817800-41829200	Weak transcription	Fetal Brain Male	brain
7	chr19:41818000-41827200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr19:41818000-41828800	Weak transcription	Hela-S3	cervix
9	chr19:41818000-41829000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:41818200-41827200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:41818200-41827200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:41818200-41827400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:41818200-41827400	Strong transcription	Osteobl	bone
14	chr19:41818200-41827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:41818200-41828400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr19:41818200-41831600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:41818400-41827200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:41818400-41827200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr19:41818400-41827400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:41818400-41827400	Strong transcription	Fetal Thymus	thymus
21	chr19:41818400-41829000	Strong transcription	Fetal Intestine Large	intestine
22	chr19:41818400-41831200	Strong transcription	Thymus	Thymus
23	chr19:41818600-41827200	Strong transcription	Lung	lung
24	chr19:41818600-41854800	Strong transcription	Dnd41	blood
25	chr19:41819000-41827200	Strong transcription	Adipose Nuclei	Adipose
26	chr19:41819000-41827400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr19:41819000-41827800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:41819000-41830600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:41819200-41829200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:41819400-41827600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:41819600-41828600	Weak transcription	Small Intestine	intestine
32	chr19:41819600-41829000	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:41819800-41827400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:41821400-41827400	Strong transcription	Liver	Liver
35	chr19:41821400-41830400	Strong transcription	Fetal Brain Female	brain
36	chr19:41821600-41827200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:41821600-41827200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr19:41821600-41827200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr19:41821600-41827400	Strong transcription	Brain Hippocampus Middle	brain
40	chr19:41821600-41830000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:41821800-41827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:41821800-41827200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr19:41821800-41827200	Strong transcription	NHEK	skin
44	chr19:41821800-41827400	Strong transcription	Brain Cingulate Gyrus	brain
45	chr19:41821800-41827400	Strong transcription	Colon Smooth Muscle	Colon
46	chr19:41821800-41827400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:41821800-41827400	Strong transcription	Pancreas	Pancrea
48	chr19:41821800-41827800	Strong transcription	Brain Angular Gyrus	brain
49	chr19:41821800-41827800	Strong transcription	GM12878-XiMat	blood
50	chr19:41821800-41828600	Strong transcription	Brain Substantia Nigra	brain

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