Variant report

Variant	rs1144540
Chromosome Location	chr19:37330613-37330614
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37327731..37330688-chr19:37341355..37343335,2	K562	blood:
2	chr19:37329288..37331381-chr19:37334889..37337614,2	K562	blood:
3	chr19:37329308..37331359-chr19:37364409..37366170,2	K562	blood:
4	chr19:37328153..37331214-chr19:37339535..37342855,6	K562	blood:
5	chr19:37327831..37331190-chr19:37339964..37343241,7	MCF-7	breast:
6	chr19:37327752..37331008-chr19:37336124..37344037,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251247	Chromatin interaction
ENSG00000197863	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1144539	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1227566	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1227588	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1673087	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs2431776	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs486221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515496	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs518196	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs526145	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs566212	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62112553	0.80[EUR][1000 genomes]
rs826278	0.86[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs826966	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv911650	chr19:37241141-37331614	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
18	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
19	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	esv3354270	chr19:37309161-37364929	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
22	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1144540	ARHGEF1	cis	cerebellum	SCAN
rs1144540	PPM1N	cis	cerebellum	SCAN
rs1144540	CATSPERG	cis	parietal	SCAN
rs1144540	ZNF529	cis	brain	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37329800-37333800	Weak transcription	Ovary	ovary
2	chr19:37329800-37334000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr19:37329800-37334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:37329800-37334000	Weak transcription	Thymus	Thymus
5	chr19:37329800-37337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:37329800-37339000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:37329800-37339600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr19:37329800-37339600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:37330000-37331000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:37330000-37331200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:37330000-37331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:37330000-37331200	Weak transcription	Psoas Muscle	Psoas
13	chr19:37330000-37331400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:37330000-37333600	Weak transcription	Primary T cells from cord blood	blood
15	chr19:37330000-37333800	Weak transcription	NH-A	brain
16	chr19:37330000-37334000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr19:37330000-37334000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr19:37330000-37334000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr19:37330000-37334000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:37330000-37334000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:37330000-37334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:37330000-37334000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:37330000-37334000	Weak transcription	Brain Substantia Nigra	brain
24	chr19:37330000-37334000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr19:37330000-37334000	Weak transcription	Fetal Muscle Leg	muscle
26	chr19:37330000-37334000	Weak transcription	Left Ventricle	heart
27	chr19:37330000-37334000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr19:37330000-37334200	Weak transcription	Fetal Stomach	stomach
29	chr19:37330000-37334200	Weak transcription	Pancreas	Pancrea
30	chr19:37330000-37334400	Weak transcription	Esophagus	oesophagus
31	chr19:37330000-37335000	Weak transcription	Fetal Thymus	thymus
32	chr19:37330000-37335200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:37330000-37336400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr19:37330000-37339600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:37330000-37340000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:37330000-37340000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:37330000-37340000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr19:37330000-37340000	Weak transcription	Fetal Brain Male	brain
39	chr19:37330000-37340000	Weak transcription	Right Ventricle	heart
40	chr19:37330000-37340400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:37330000-37340400	Weak transcription	Colonic Mucosa	Colon
42	chr19:37330000-37340400	Weak transcription	Placenta	Placenta
43	chr19:37330000-37340400	Weak transcription	Stomach Mucosa	stomach
44	chr19:37330000-37340600	Weak transcription	Gastric	stomach
45	chr19:37330000-37340600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr19:37330000-37340600	Weak transcription	Spleen	Spleen
47	chr19:37330000-37340600	Weak transcription	HSMM	muscle
48	chr19:37330200-37331000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr19:37330200-37331000	Weak transcription	Liver	Liver
50	chr19:37330200-37331200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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