Variant report

Variant	rs7251246
Chromosome Location	chr19:41227106-41227107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41220314-41228780	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:41220376-41228744	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF143	chr19:41227088-41227272	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41219786..41224599-chr19:41225550..41230033,6	K562	blood:
2	chr19:41225203..41228152-chr19:41229042..41232599,3	MCF-7	breast:
3	chr19:41225475..41227295-chr19:41243418..41244971,2	K562	blood:
4	chr19:41225224..41227952-chr19:41245122..41248446,3	MCF-7	breast:
5	chr19:41224721..41227148-chr19:41302837..41304471,2	K562	blood:
6	chr19:41224929..41227139-chr19:41232897..41235326,2	K562	blood:
7	chr19:41220671..41224766-chr19:41226443..41229963,4	K562	blood:
8	chr19:41168010..41170261-chr19:41227028..41229783,2	MCF-7	breast:
9	chr19:41226837..41229438-chr19:41260513..41263205,2	MCF-7	breast:
10	chr19:41225019..41226612-chr19:41226846..41228411,3	MCF-7	breast:

No data

Variant related genes	Relation type
ADCK4	TF binding region
ENSG00000188493	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10407351	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10425765	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11548478	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12976551	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469427	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1870086	0.82[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1870087	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2115239	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2246095	0.91[JPT][hapmap]
rs2288451	0.85[CEU][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2290692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2290693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2369302	0.82[JPT][hapmap]
rs2604885	0.91[JPT][hapmap]
rs3745210	0.83[ASN][1000 genomes]
rs3745211	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745216	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.80[ASN][1000 genomes]
rs3865452	0.91[JPT][hapmap]
rs4802085	0.96[CEU][hapmap];0.91[JPT][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4802086	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802087	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803360	0.85[EUR][1000 genomes]
rs7248468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257602	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7260405	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111960	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs890934	0.87[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.86[AFR][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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7251246	C19orf54	cis	Nerve Tibial	GTEx
rs7251246	ADCK4	cis	Nerve Tibial	GTEx
rs7251246	LIN7B	cis	parietal	SCAN
rs7251246	KCNN4	cis	cerebellum	SCAN
rs7251246	ZNF574	cis	parietal	SCAN
rs7251246	SYMPK	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41223400-41227200	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr19:41223400-41227200	Flanking Active TSS	HUVEC	blood vessel
3	chr19:41223400-41227400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:41224000-41227200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:41224400-41227200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:41224400-41227200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr19:41224600-41227200	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr19:41224800-41228600	Enhancers	Fetal Brain Male	brain
9	chr19:41225000-41227200	Enhancers	Fetal Heart	heart
10	chr19:41225000-41228400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:41225200-41227200	Enhancers	Ovary	ovary
12	chr19:41225200-41227200	Enhancers	Spleen	Spleen
13	chr19:41225200-41227400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:41225200-41228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:41225200-41229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:41225200-41229400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:41225200-41235200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:41225400-41227200	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr19:41225400-41227200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
22	chr19:41225400-41231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr19:41225600-41227200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:41225600-41227200	Enhancers	Fetal Thymus	thymus
25	chr19:41225600-41229800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:41225600-41231600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:41225800-41227200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:41225800-41228000	Weak transcription	A549	lung
29	chr19:41225800-41228200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr19:41225800-41228400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:41225800-41229600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:41225800-41229800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr19:41225800-41229800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:41225800-41229800	Weak transcription	Thymus	Thymus
35	chr19:41225800-41232000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:41225800-41232200	Weak transcription	Fetal Kidney	kidney
37	chr19:41225800-41233400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr19:41225800-41233400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr19:41225800-41236400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr19:41226000-41227200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:41226200-41227200	Flanking Active TSS	Psoas Muscle	Psoas
42	chr19:41226200-41227200	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr19:41226200-41227200	Flanking Active TSS	HMEC	breast
44	chr19:41226200-41227200	Flanking Active TSS	NHLF	lung
45	chr19:41226200-41227200	Flanking Active TSS	Osteobl	bone
46	chr19:41226400-41227200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
47	chr19:41226400-41227200	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr19:41226400-41227200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:41226400-41227200	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr19:41226400-41227200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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