Variant report

Variant	rs2075754
Chromosome Location	chr19:42375244-42375245
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42374454..42377744-chr19:42431362..42433284,5	K562	blood:
2	chr19:42373799..42381047-chr19:42460989..42465067,14	K562	blood:
3	chr19:42374516..42378766-chr19:42444244..42446935,5	K562	blood:
4	chr19:42354421..42356282-chr19:42374725..42377333,2	MCF-7	breast:
5	chr19:42374823..42377954-chr19:42385843..42389445,4	MCF-7	breast:
6	chr19:42373353..42379670-chr19:42459996..42464717,12	K562	blood:
7	chr19:42374516..42376922-chr19:42442141..42445764,4	K562	blood:
8	chr19:42371951..42373649-chr19:42373763..42375308,2	MCF-7	breast:
9	chr19:42374905..42377918-chr19:42453712..42457623,5	K562	blood:
10	chr19:42374905..42378139-chr19:42452312..42458975,8	K562	blood:
11	chr19:42311919..42314019-chr19:42373613..42376038,2	K562	blood:
12	chr19:42373255..42375761-chr19:42417935..42419997,2	K562	blood:
13	chr19:42311919..42314958-chr19:42372358..42376038,3	K562	blood:
14	chr19:42374727..42377526-chr19:42531576..42534265,2	MCF-7	breast:
15	chr19:42374489..42376013-chr8:101732709..101734886,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000076928	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000070756	Chromatin interaction
ENSG00000170956	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10404939	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap]
rs10405900	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10408367	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10414356	0.81[ASN][1000 genomes]
rs10414823	0.95[CHB][hapmap];0.89[YRI][hapmap]
rs10415452	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10416824	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.94[YRI][hapmap]
rs10417985	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10500284	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12461099	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12461131	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12976571	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12979253	0.95[CHB][hapmap];0.81[CHD][hapmap]
rs12984383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1366610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1428922	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1457144	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap]
rs1870092	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs2008798	0.90[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap]
rs2075749	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075750	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075752	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2199829	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2290695	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs2305809	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3786536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786538	0.93[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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3810153	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs3922888	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4130852	0.81[ASN][1000 genomes]
rs4803511	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4803512	0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs58857981	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6509001	0.82[ASN][1000 genomes]
rs6509002	0.91[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs7250787	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251336	0.82[CHB][hapmap]
rs7251960	0.82[CHB][hapmap]
rs7254214	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257666	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258163	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7259596	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259967	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs734107	0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap]
rs73549152	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102670	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8104958	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap]
rs8106505	0.95[CHB][hapmap]
rs8113283	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs8113641	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs873282	0.93[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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs882520	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs891167	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs899662	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs930102	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv932623	chr19:42370540-42378620	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2075754	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs2075754	LIG1	cis	parietal	SCAN
rs2075754	SLC1A5	cis	parietal	SCAN
rs2075754	RPS19	cis	Esophagus Muscularis	GTEx
rs2075754	GLTSCR2	cis	cerebellum	SCAN
rs2075754	ZNF575	cis	parietal	SCAN
rs2075754	EXOC3L2	cis	cerebellum	SCAN
rs2075754	PPP5C	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42365400-42376200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:42365400-42376600	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr19:42366000-42376000	Strong transcription	HSMMtube	muscle
4	chr19:42366400-42377600	Strong transcription	Fetal Brain Female	brain
5	chr19:42367000-42376600	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr19:42367000-42376800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42367200-42377200	Strong transcription	Brain Inferior Temporal Lobe	brain
8	chr19:42367400-42375600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:42367600-42375600	Strong transcription	Right Ventricle	heart
10	chr19:42367600-42376200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:42367600-42379200	Weak transcription	Fetal Brain Male	brain
12	chr19:42367800-42375800	Strong transcription	Left Ventricle	heart
13	chr19:42367800-42376200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:42368400-42376600	Strong transcription	Brain Cingulate Gyrus	brain
15	chr19:42368600-42376200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:42368800-42376200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:42368800-42376200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr19:42368800-42377000	Strong transcription	Fetal Stomach	stomach
19	chr19:42368800-42377400	Strong transcription	Brain Germinal Matrix	brain
20	chr19:42369000-42376800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:42369000-42376800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr19:42369200-42376200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:42369200-42377200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:42369400-42376600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:42369400-42377600	Genic enhancers	Fetal Thymus	thymus
26	chr19:42369600-42375400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:42369600-42376400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:42369600-42376400	Strong transcription	HUVEC	blood vessel
29	chr19:42369600-42376600	Strong transcription	HSMM	muscle
30	chr19:42369600-42377400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:42369600-42386400	Weak transcription	Fetal Kidney	kidney
32	chr19:42370200-42375600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:42370400-42377600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:42370600-42376200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:42370800-42375400	Genic enhancers	A549	lung
36	chr19:42370800-42376200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:42370800-42376800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:42371000-42376400	Strong transcription	HMEC	breast
39	chr19:42371600-42376600	Strong transcription	Lung	lung
40	chr19:42371800-42375400	Genic enhancers	Primary T cells from cord blood	blood
41	chr19:42371800-42375400	Strong transcription	Hela-S3	cervix
42	chr19:42371800-42375600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr19:42371800-42376400	Strong transcription	Adipose Nuclei	Adipose
44	chr19:42371800-42376400	Strong transcription	Brain Substantia Nigra	brain
45	chr19:42371800-42376400	Genic enhancers	Rectal Mucosa Donor 31	rectum
46	chr19:42371800-42376600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:42372000-42376200	Strong transcription	Aorta	Aorta
48	chr19:42372000-42376400	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr19:42372000-42376600	Strong transcription	Brain Hippocampus Middle	brain
50	chr19:42372000-42376600	Strong transcription	Placenta Amnion	Placenta Amnion

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