Variant report

Variant	rs6957
Chromosome Location	chr19:41830606-41830607
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41828482..41836150-chr19:41836490..41842395,12	K562	blood:
2	chr19:41811198..41813629-chr19:41830281..41833026,2	K562	blood:
3	chr19:41826823..41830968-chr19:41831922..41834042,4	K562	blood:
4	chr19:41767636..41772705-chr19:41827976..41830874,5	K562	blood:
5	chr19:41828559..41831020-chr19:41944641..41946935,2	MCF-7	breast:
6	chr19:41814818..41818108-chr19:41828444..41830953,5	K562	blood:
7	chr19:41829468..41831265-chr19:41933242..41935169,2	MCF-7	breast:
8	chr19:41813217..41816431-chr19:41827201..41830694,5	MCF-7	breast:
9	chr19:41827333..41835079-chr19:41855373..41860241,10	K562	blood:
10	chr19:41827408..41831164-chr19:41901595..41905295,3	MCF-7	breast:
11	chr19:41825452..41832651-chr19:41855170..41863054,16	K562	blood:

No data

Variant related genes	Relation type
ENSG00000142039	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000105341	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10410836	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10421990	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1056854	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs11466347	0.83[EUR][1000 genomes]
rs11466359	0.98[EUR][1000 genomes]
rs11879562	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11880564	0.98[EUR][1000 genomes]
rs11881940	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs11881953	0.82[EUR][1000 genomes]
rs11882467	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12327659	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462203	0.85[CHB][hapmap]
rs12972266	0.92[EUR][1000 genomes]
rs12974323	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12974420	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs12975585	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12975920	0.95[ASN][1000 genomes]
rs12976536	0.86[EUR][1000 genomes]
rs12978323	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12980298	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12980480	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12980839	0.92[ASN][1000 genomes]
rs12980942	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12981053	0.86[EUR][1000 genomes]
rs12983047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984160	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs12985162	0.91[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs12985339	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs13345456	0.97[ASN][1000 genomes]
rs16958994	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958996	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958999	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865052	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865053	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053086	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2241718	1.00[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs2241719	0.98[EUR][1000 genomes]
rs2241720	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2304230	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304234	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs34075897	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34322801	0.93[EUR][1000 genomes]
rs34945449	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35501756	0.95[EUR][1000 genomes]
rs35812313	0.86[EUR][1000 genomes]
rs3745295	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752705	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816052	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3826714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456618	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]
rs4802111	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs4802112	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4802113	0.84[CHB][hapmap]
rs4803448	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs4803449	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6508974	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs66724427	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67511749	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67744888	0.86[EUR][1000 genomes]
rs7245398	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246525	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7248164	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254679	0.82[CEU][hapmap];0.92[ASN][1000 genomes]
rs7256416	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256856	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257310	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257742	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257825	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7258749	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8103839	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs8105161	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105901	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs8109167	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109627	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6957	FLT3LG	cis	cerebellum	SCAN
rs6957	PLEKHA4	cis	cerebellum	SCAN
rs6957	BAX	cis	cerebellum	SCAN
rs6957	TSKS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41818200-41831600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:41818400-41831200	Strong transcription	Thymus	Thymus
3	chr19:41818600-41854800	Strong transcription	Dnd41	blood
4	chr19:41822400-41831000	Weak transcription	Psoas Muscle	Psoas
5	chr19:41823200-41832000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:41823400-41830800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:41823400-41832200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:41824400-41834000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:41824600-41830800	Genic enhancers	Spleen	Spleen
10	chr19:41827000-41830800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:41827000-41832800	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr19:41827200-41832000	Enhancers	NHDF-Ad	bronchial
13	chr19:41827400-41830800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr19:41827400-41831000	Enhancers	Ovary	ovary
15	chr19:41827400-41831000	Flanking Active TSS	HepG2	liver
16	chr19:41827400-41831200	Weak transcription	Aorta	Aorta
17	chr19:41827400-41831200	Enhancers	Left Ventricle	heart
18	chr19:41827400-41833000	Enhancers	Primary hematopoietic stem cells	blood
19	chr19:41827400-41833000	Genic enhancers	Fetal Thymus	thymus
20	chr19:41827600-41831800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr19:41827800-41830800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr19:41827800-41832200	Enhancers	Stomach Mucosa	stomach
23	chr19:41828000-41832000	Enhancers	Duodenum Mucosa	Duodenum
24	chr19:41828200-41831200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr19:41828400-41832200	Enhancers	Liver	Liver
26	chr19:41828600-41830800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr19:41828600-41831200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:41828600-41831200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr19:41828600-41832200	Enhancers	Primary B cells from cord blood	blood
30	chr19:41828600-41834000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr19:41828800-41831200	Enhancers	Colon Smooth Muscle	Colon
32	chr19:41828800-41831600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:41828800-41832400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:41828800-41834000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:41828800-41834400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:41829000-41830800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:41829000-41831000	Weak transcription	Small Intestine	intestine
38	chr19:41829000-41831200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:41829000-41831200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr19:41829200-41830800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr19:41829200-41830800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:41829200-41830800	Enhancers	Brain Substantia Nigra	brain
43	chr19:41829200-41831600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:41829200-41832200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:41829200-41835400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr19:41829400-41831000	Enhancers	Rectal Smooth Muscle	rectum
47	chr19:41829400-41831200	Enhancers	Adipose Nuclei	Adipose
48	chr19:41829400-41831200	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr19:41829400-41831600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:41829400-41831600	Enhancers	HUVEC	blood vessel

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