Variant report

Variant	rs16970649
Chromosome Location	chr19:36222857-36222858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36219393-36224196	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:36222359-36222898	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:36222798-36222858	K562	blood:	n/a	n/a
4	POLR2A	chr19:36222491-36222867	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:36222359-36222990	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:36222761-36222939	K562	blood:	n/a	n/a
7	POLR2A	chr19:36222394-36222870	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr19:36221950-36222989	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:36222452-36222869	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36220754..36223608-chr19:36241225..36243043,2	MCF-7	breast:
2	chr19:36220761..36223012-chr19:36264330..36266140,2	MCF-7	breast:

Variant related genes	Relation type
KMT2B	TF binding region
ENSG00000004777	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11546662	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11546665	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11882996	0.80[ASW][hapmap]
rs17776834	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2227278	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];0.86[MKK][hapmap];0.94[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2234360	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];0.86[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2234375	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267585	0.80[EUR][1000 genomes]
rs2267586	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2285420	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs34562867	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817622	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893069	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580318	0.80[EUR][1000 genomes]
rs4992668	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56849855	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57180990	0.80[EUR][1000 genomes]
rs58142685	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58255615	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58496446	0.80[EUR][1000 genomes]
rs58952294	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs61254015	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs61351824	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61375471	0.80[EUR][1000 genomes]
rs73590543	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590544	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73590559	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590561	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590564	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73590568	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590576	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590585	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590591	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590598	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73592416	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73592448	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73592461	0.83[EUR][1000 genomes]
rs73599286	0.80[EUR][1000 genomes]
rs73599289	0.80[EUR][1000 genomes]
rs73600880	0.80[EUR][1000 genomes]
rs73600881	0.80[EUR][1000 genomes]
rs73600885	0.81[EUR][1000 genomes]
rs73600893	0.80[EUR][1000 genomes]
rs73600899	0.87[EUR][1000 genomes]
rs73602803	0.88[EUR][1000 genomes]
rs73602804	0.88[EUR][1000 genomes]
rs73602806	0.88[EUR][1000 genomes]
rs73602823	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73602827	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73602832	0.93[EUR][1000 genomes]
rs73602833	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv515536	chr19:36219525-36240960	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16970649	TEX101	cis	parietal	SCAN
rs16970649	PLD3	cis	cerebellum	SCAN
rs16970649	DPF1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36210600-36223000	Strong transcription	Fetal Lung	lung
2	chr19:36210600-36223000	Strong transcription	Rectal Smooth Muscle	rectum
3	chr19:36210600-36223400	Strong transcription	Primary T cells from cord blood	blood
4	chr19:36210600-36230000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr19:36210600-36230200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr19:36210600-36230200	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr19:36210600-36230200	Strong transcription	Ovary	ovary
8	chr19:36210600-36230200	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:36210600-36230400	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr19:36210600-36230400	Strong transcription	A549	lung
11	chr19:36210600-36230600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:36210600-36230600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:36210600-36230600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:36210600-36230600	Weak transcription	Right Atrium	heart
15	chr19:36210600-36230600	Strong transcription	NHLF	lung
16	chr19:36210600-36231200	Weak transcription	Fetal Brain Male	brain
17	chr19:36210800-36223600	Strong transcription	Colon Smooth Muscle	Colon
18	chr19:36210800-36225000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr19:36210800-36227400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr19:36210800-36228000	Strong transcription	Fetal Thymus	thymus
21	chr19:36210800-36229600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr19:36210800-36229800	Strong transcription	Adipose Nuclei	Adipose
23	chr19:36210800-36230000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:36210800-36230200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:36210800-36230200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:36210800-36230200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:36210800-36230200	Strong transcription	Fetal Intestine Large	intestine
28	chr19:36210800-36230200	Strong transcription	Gastric	stomach
29	chr19:36210800-36230200	Strong transcription	Thymus	Thymus
30	chr19:36210800-36230400	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr19:36210800-36230400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr19:36210800-36230400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr19:36210800-36230400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:36210800-36230400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:36210800-36230400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:36210800-36230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:36210800-36230400	Strong transcription	Brain Cingulate Gyrus	brain
38	chr19:36210800-36230400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:36210800-36230400	Strong transcription	Colonic Mucosa	Colon
40	chr19:36210800-36230600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr19:36210800-36231000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:36211000-36223400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:36211000-36225200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:36211000-36227600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:36211000-36230000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr19:36211000-36230000	Strong transcription	Left Ventricle	heart
47	chr19:36211000-36230200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:36211000-36230200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:36211000-36230200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr19:36211000-36230200	Strong transcription	Osteobl	bone

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