Variant report

Variant	rs4456618
Chromosome Location	chr19:41813957-41813958
allele	C/G
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	chr19:41813835-41814847	A549	lung:	n/a	n/a
2	POLR2A	chr19:41813814-41814889	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:41811701-41817543	SK-N-MC	brain:	n/a	n/a
4	CTCF	chr19:41811702-41817527	A549	lung:	n/a	chr19:41814589-41814607 chr19:41814590-41814606 chr19:41814584-41814605 chr19:41814591-41814604 chr19:41814591-41814604 chr19:41813852-41813873 chr19:41813850-41813868 chr19:41814601-41814614
5	POLR2A	chr19:41813891-41813995	MCF-7	breast:	n/a	n/a
6	SMC3	chr19:41813494-41815570	SK-N-SH	brain:	n/a	chr19:41814591-41814605
7	POLR2A	chr19:41813221-41816825	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:41813405-41816912	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:41813668-41816626	GM18505	blood:	n/a	n/a
10	POLR2A	chr19:41813712-41816830	GM12891	blood:	n/a	n/a
11	CTCF	chr19:41813840-41813990	RPTEC	kidney:	n/a	chr19:41813852-41813873 chr19:41813850-41813868
12	POLR2A	chr19:41813813-41815574	GM12891	blood:	n/a	n/a
13	STAT5A	chr19:41813753-41816690	GM12878	blood:	n/a	chr19:41814315-41814323 chr19:41813977-41813985 chr19:41816016-41816024
14	POLR2A	chr19:41809524-41818013	K562	blood:	n/a	n/a
15	POLR2A	chr19:41813354-41817333	K562	blood:	n/a	n/a
16	POLR2A	chr19:41813852-41814206	HUVEC	blood vessel:	n/a	n/a
17	CTCF	chr19:41813840-41813990	HEK293	kidney:	n/a	chr19:41813852-41813873 chr19:41813850-41813868
18	BCL3	chr19:41813942-41815083	K562	blood:	n/a	chr19:41814588-41814596
19	CTCF	chr19:41813820-41813970	GM12878	blood:	n/a	chr19:41813852-41813873 chr19:41813850-41813868
20	POLR2A	chr19:41812504-41817492	U87	brain:	n/a	n/a
21	POLR2A	chr19:41813949-41814835	GM15510	blood:	n/a	n/a
22	MAX	chr19:41813797-41817106	A549	lung:	n/a	n/a
23	POLR2A	chr19:41813633-41816880	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:41813724-41815833	HL-60	blood:	n/a	n/a
25	POLR2A	chr19:41813664-41816817	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr19:41813202-41816983	A549	lung:	n/a	n/a
27	POLR2A	chr19:41813807-41814004	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr19:41813845-41814863	A549	lung:	n/a	n/a
29	POLR2A	chr19:41813951-41813961	MCF-7	breast:	n/a	n/a
30	POLR2A	chr19:41813044-41816956	K562	blood:	n/a	n/a
31	POLR2A	chr19:41812949-41815614	K562	blood:	n/a	n/a
32	ETS1	chr19:41813898-41814864	A549	lung:	n/a	chr19:41814666-41814673 chr19:41814583-41814596
33	POLR2A	chr19:41813768-41817133	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr19:41813358-41817263	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr19:41813811-41814918	A549	lung:	n/a	n/a
36	PBX3	chr19:41813734-41817130	A549	lung:	n/a	chr19:41815964-41815973
37	BCL3	chr19:41813653-41817132	A549	lung:	n/a	chr19:41815872-41815881 chr19:41814588-41814596
38	POLR2A	chr19:41813847-41816723	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr19:41813675-41817544	K562	blood:	n/a	n/a
40	POLR2A	chr19:41813733-41815737	H1-hESC	embryonic stem cell:	n/a	n/a
41	REST	chr19:41813710-41814102	A549	lung:	n/a	chr19:41813960-41813980 chr19:41813971-41813980 chr19:41813960-41813980 chr19:41813960-41813980
42	CTCF	chr19:41813920-41814070	HAc	cerebellar:	n/a	n/a
43	TCF12	chr19:41813636-41817113	A549	lung:	n/a	n/a
44	PML	chr19:41813647-41816876	GM12878	blood:	n/a	chr19:41816305-41816313
45	POLR2A	chr19:41813800-41815658	HepG2	liver:	n/a	n/a
46	CTCF	chr19:41813840-41813990	HepG2	liver:	n/a	chr19:41813852-41813873 chr19:41813850-41813868
47	POLR2A	chr19:41813811-41816926	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:41813719-41817446	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:41813885-41815505	GM12878	blood:	n/a	n/a
50	NFATC1	chr19:41813426-41814089	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41799355..41806261-chr19:41812914..41817863,9	MCF-7	breast:
2	chr19:41808201..41810426-chr19:41812838..41816052,5	K562	blood:
3	chr19:41766963..41771332-chr19:41813075..41817628,7	K562	blood:
4	chr19:41711943..41714623-chr19:41813301..41815470,3	MCF-7	breast:
5	chr19:41813131..41816938-chr19:41856231..41860417,4	MCF-7	breast:
6	chr19:41767589..41772847-chr19:41812402..41817981,15	MCF-7	breast:
7	chr19:41766631..41773289-chr19:41812153..41817614,9	K562	blood:
8	chr19:41801720..41806546-chr19:41809215..41814185,5	MCF-7	breast:

Variant related genes	Relation type
CCDC97	TF binding region
ENSG00000105329	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000142046	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10410836	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10421990	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056854	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11466359	0.92[EUR][1000 genomes]
rs11879562	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880564	0.92[EUR][1000 genomes]
rs11881940	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs11881953	0.88[EUR][1000 genomes]
rs11882467	0.95[CHB][hapmap]
rs12327659	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462203	0.90[CHB][hapmap]
rs12972266	0.98[EUR][1000 genomes]
rs12974323	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974420	0.91[CEU][hapmap];0.80[CHB][hapmap];0.92[EUR][1000 genomes]
rs12975585	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12975920	0.98[ASN][1000 genomes]
rs12976536	0.92[EUR][1000 genomes]
rs12978323	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12980298	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12980480	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980839	0.94[ASN][1000 genomes]
rs12980942	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12981053	0.81[EUR][1000 genomes]
rs12983047	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12984160	1.00[CEU][hapmap];0.80[CHB][hapmap];0.98[EUR][1000 genomes]
rs12985162	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs12985339	0.91[CEU][hapmap];0.80[CHB][hapmap];0.92[EUR][1000 genomes]
rs13345456	1.00[ASN][1000 genomes]
rs16958994	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958996	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958999	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1865051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1865052	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1865053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053086	0.91[CEU][hapmap];0.80[CHB][hapmap];0.92[EUR][1000 genomes]
rs2241718	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2241719	0.92[EUR][1000 genomes]
rs2241720	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2304230	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304234	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs34075897	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34322801	0.94[EUR][1000 genomes]
rs34945449	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35501756	0.95[EUR][1000 genomes]
rs35812313	0.92[EUR][1000 genomes]
rs3745295	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752705	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786555	0.81[ASN][1000 genomes]
rs3816052	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802111	0.90[CHB][hapmap]
rs4802112	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs4802113	0.89[CHB][hapmap]
rs4803448	0.90[CHB][hapmap]
rs4803449	0.90[CHB][hapmap]
rs6508974	0.90[CHB][hapmap]
rs66724427	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67511749	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67744888	0.92[EUR][1000 genomes]
rs6957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7245398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246525	0.90[CHB][hapmap]
rs7248164	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254679	0.83[CEU][hapmap];0.94[ASN][1000 genomes]
rs7256416	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256856	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257310	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]
rs7257742	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7257825	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258749	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103839	0.91[CEU][hapmap];0.80[CHB][hapmap];0.92[EUR][1000 genomes]
rs8105161	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105901	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[EUR][1000 genomes]
rs8109167	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109627	0.95[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv17637	chr19:41770228-41815282	Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41773200-41814400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41773800-41814200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:41773800-41814200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr19:41773800-41814200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:41774000-41814200	Strong transcription	Fetal Brain Female	brain
6	chr19:41780200-41815800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:41783800-41814400	Strong transcription	Brain Germinal Matrix	brain
8	chr19:41788600-41815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:41795200-41814000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:41795400-41814200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:41795600-41814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:41801600-41814600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:41802600-41814200	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr19:41803200-41814400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:41803200-41814400	Strong transcription	HMEC	breast
16	chr19:41804800-41814200	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr19:41805000-41814200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:41805200-41814200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:41805200-41814400	Strong transcription	Gastric	stomach
20	chr19:41805400-41814200	Strong transcription	Fetal Intestine Large	intestine
21	chr19:41805600-41814200	Strong transcription	Fetal Intestine Small	intestine
22	chr19:41806200-41814000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:41806200-41814000	Strong transcription	Brain Angular Gyrus	brain
24	chr19:41806200-41814200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:41806200-41814200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:41806200-41814200	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr19:41806200-41814200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:41806200-41814200	Strong transcription	Fetal Stomach	stomach
29	chr19:41806200-41814200	Strong transcription	NH-A	brain
30	chr19:41806200-41814400	Strong transcription	Fetal Lung	lung
31	chr19:41806200-41814400	Strong transcription	Osteobl	bone
32	chr19:41806200-41814600	Strong transcription	HSMM	muscle
33	chr19:41806400-41814000	Strong transcription	HSMMtube	muscle
34	chr19:41806600-41814000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:41806800-41814000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:41806800-41814000	Weak transcription	Right Atrium	heart
37	chr19:41807800-41814200	Strong transcription	Left Ventricle	heart
38	chr19:41808000-41814400	Genic enhancers	Fetal Thymus	thymus
39	chr19:41810000-41814400	Genic enhancers	Duodenum Mucosa	Duodenum
40	chr19:41810000-41814400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr19:41810600-41814000	Strong transcription	Placenta	Placenta
42	chr19:41810800-41814200	Strong transcription	Esophagus	oesophagus
43	chr19:41811000-41814000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr19:41811000-41814200	Weak transcription	Hela-S3	cervix
45	chr19:41811200-41814600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:41811400-41814000	Weak transcription	Fetal Heart	heart
47	chr19:41812200-41814200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr19:41812200-41814400	Weak transcription	Fetal Kidney	kidney
49	chr19:41812200-41814600	Genic enhancers	Rectal Mucosa Donor 29	rectum
50	chr19:41812400-41814200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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