Variant report

Variant	rs4421195
Chromosome Location	chr6:53599269-53599270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53587433..53591147-chr6:53595586..53599292,4	MCF-7	breast:
2	chr6:53516373..53518187-chr6:53597538..53600553,4	MCF-7	breast:
3	chr6:53411604..53413462-chr6:53597893..53600161,2	MCF-7	breast:
4	chr6:53595711..53597938-chr6:53598268..53600839,2	MCF-7	breast:
5	chr6:53590810..53593190-chr6:53597036..53600341,4	K562	blood:
6	chr6:53598898..53601641-chr6:53603723..53606379,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13197492	0.80[EUR][1000 genomes]
rs3000998	0.82[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs35709775	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4269375	0.82[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4276503	0.81[EUR][1000 genomes]
rs4342426	0.81[EUR][1000 genomes]
rs4475321	0.81[EUR][1000 genomes]
rs4493745	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4518484	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4715425	0.82[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs5001609	0.81[EUR][1000 genomes]
rs6458960	0.80[EUR][1000 genomes]
rs7738167	0.89[EUR][1000 genomes]
rs7744954	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7756654	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756771	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756797	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7763012	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7767443	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs9382239	0.82[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4421195	C6orf142	cis	cerebellum	SCAN
rs4421195	IL17A	cis	parietal	SCAN
rs4421195	HMGCLL1	cis	parietal	SCAN
rs4421195	LRRC1	cis	parietal	SCAN
rs4421195	PKHD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53589800-53599400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:53591200-53599600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr6:53591200-53599800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:53591600-53599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:53593000-53599800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:53593600-53599400	Enhancers	Hela-S3	cervix
7	chr6:53593600-53599400	Weak transcription	HSMMtube	muscle
8	chr6:53593600-53599800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr6:53593600-53600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:53593800-53599800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:53594600-53599600	Weak transcription	Placenta	Placenta
12	chr6:53595000-53599800	Enhancers	Dnd41	blood
13	chr6:53595400-53599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:53596000-53599400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:53596000-53599600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:53596000-53599600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:53596000-53601600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:53596000-53605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:53597200-53599600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:53597200-53599600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:53597200-53599800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:53597200-53604000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:53597400-53599400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:53597400-53599400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:53597400-53599400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:53597400-53599400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:53597400-53599800	Weak transcription	Primary T cells from cord blood	blood
28	chr6:53597400-53599800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:53597400-53600000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:53597800-53599400	Weak transcription	Fetal Thymus	thymus
31	chr6:53597800-53599400	Weak transcription	Thymus	Thymus
32	chr6:53597800-53599600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:53598400-53601000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:53598400-53601200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:53598400-53601400	Enhancers	Fetal Intestine Small	intestine
36	chr6:53598400-53603000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:53598600-53601400	Enhancers	Fetal Intestine Large	intestine
38	chr6:53599000-53600000	Enhancers	Stomach Mucosa	stomach
39	chr6:53599000-53600400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr6:53599000-53601000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:53599200-53599400	Flanking Active TSS	HMEC	breast
42	chr6:53599200-53599400	Enhancers	NH-A	brain
43	chr6:53599200-53599400	Flanking Active TSS	NHEK	skin
44	chr6:53599200-53599600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr6:53599200-53599800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr6:53599200-53599800	Flanking Active TSS	HUVEC	blood vessel
47	chr6:53599200-53600000	Flanking Active TSS	A549	lung
48	chr6:53599200-53600600	Enhancers	HSMM	muscle
49	chr6:53599200-53601200	Enhancers	Duodenum Mucosa	Duodenum
50	chr6:53599200-53603000	Enhancers	Fetal Heart	heart

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