Variant report

Variant	esv3445398
Chromosome Location	chrX:55172929-55185618
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:55172107..55173217-chrX:55185088..55186125,3	MCF-7	breast:
2	chrX:55172107..55173217-chrX:55185088..55186125,3	MCF-7	breast:
3	chrX:55182714..55184478-chrX:55187112..55188785,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM104B-1	chrX:55185555-55185661	NONHSAT137240
2	lnc-FAM104B-1	chrX:55185562-55185661	NONHSAT137241

Variant related genes	Relation type
ENSG00000182518	chromatin interactions

Extended variants
information (count: 172 )
Associated
traits (count: 41 )

Variant overlapped rSNPs/rCNVs (count:172 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs79006947	chrX:55172939-55172940	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs186190057	chrX:55172972-55172973	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs5960062	chrX:55172973-55172974	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs191427621	chrX:55173046-55173047	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs180755083	chrX:55173322-55173323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs185132983	chrX:55173472-55173473	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs73492451	chrX:55173523-55173524	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs189838665	chrX:55173569-55173570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs143550223	chrX:55173626-55173627	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs138056134	chrX:55173698-55173699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs183157127	chrX:55173719-55173720	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs11327722	chrX:55173733-55173734	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs187951986	chrX:55173820-55173821	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs115109390	chrX:55173963-55173964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs191554202	chrX:55174042-55174043	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs112534190	chrX:55174067-55174068	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs34896492	chrX:55174068-55174069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs78290949	chrX:55174086-55174087	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs76816900	chrX:55174088-55174089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs76920144	chrX:55174089-55174090	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs77146675	chrX:55174090-55174091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs376812458	chrX:55174093-55174094	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs2453230	chrX:55174122-55174123	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs2453231	chrX:55174128-55174129	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs2498463	chrX:55174147-55174148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs2453232	chrX:55174155-55174156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs111561879	chrX:55174156-55174157	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs2453233	chrX:55174158-55174159	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs564272481	chrX:55174192-55174193	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs35458306	chrX:55174204-55174205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs571260962	chrX:55174211-55174212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs34260900	chrX:55174217-55174218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs35829553	chrX:55174220-55174221	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs34223286	chrX:55174241-55174242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs183720264	chrX:55174243-55174244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs34265256	chrX:55174256-55174257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs7058903	chrX:55174638-55174639	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs113402057	chrX:55174794-55174795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs7061355	chrX:55174954-55174955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs7061471	chrX:55175033-55175034	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs72202714	chrX:55175169-55175170	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs113300327	chrX:55175171-55175172	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs532322316	chrX:55175320-55175321	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs539326947	chrX:55175333-55175334	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs2498464	chrX:55175362-55175363	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs2498465	chrX:55175401-55175402	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs2498466	chrX:55175410-55175411	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs192958718	chrX:55175493-55175494	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs183670540	chrX:55175497-55175498	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs201479207	chrX:55175605-55175606	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:41)

Disease	PMID	Source
Cancer	21637783	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Cancer	16751803	CNVD
Intellectual disability	23615299	CNVD
Neuroblastoma	18923191	CNVD
Burkitt''s lymphoma	20823134	CNVD
Astrocytoma	17387387	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	21979893	CNVD
Schizophrenia	23904455	CNVD
Olfactory neuroblastoma	18408657	CNVD
infertile	22614455	CNVD
Acute myeloid leukemia	20729466	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute myeloid leukemia	21251322	CNVD
Cancer	20581869	CNVD
Multiple myeloma	20724749	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Lung cancer	18438408	CNVD
Cancer	20164919	CNVD
Premature ovarian failure	20952765	CNVD
Thyroid cancer	19087340	CNVD
lymphocytic leukemia	21291569	CNVD
Cervical cancer	21062161	CNVD
Follicular lymphoma	20505157	CNVD
primary effusion lymphomas	17116491	CNVD
Testicular germ cell tumor	18059402	CNVD
Testicular cancer	18059402	CNVD
Seminomas	18059402	CNVD
Breast cancer	21785460	CNVD
Ovarian cancer	19835627	CNVD
Mental retardation	21735175	CNVD

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:55167600-55187000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chrX:55169400-55175400	Weak transcription	Fetal Intestine Large	intestine
3	chrX:55169400-55186600	Weak transcription	Fetal Intestine Small	intestine
4	chrX:55169400-55186800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chrX:55170800-55186200	Weak transcription	A549	lung
6	chrX:55171400-55186800	Weak transcription	Stomach Mucosa	stomach
7	chrX:55172600-55186200	Weak transcription	Brain Germinal Matrix	brain
8	chrX:55172800-55173200	Weak transcription	Thymus	Thymus
9	chrX:55172800-55173600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chrX:55172800-55175000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chrX:55172800-55176000	Weak transcription	Fetal Muscle Leg	muscle
12	chrX:55172800-55176600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chrX:55172800-55176600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chrX:55172800-55176800	Weak transcription	Gastric	stomach
15	chrX:55172800-55176800	Weak transcription	Lung	lung
16	chrX:55172800-55181200	Weak transcription	Esophagus	oesophagus
17	chrX:55172800-55181400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chrX:55172800-55183400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chrX:55172800-55183600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chrX:55172800-55185400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chrX:55172800-55185400	Weak transcription	Brain Substantia Nigra	brain
22	chrX:55172800-55185600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chrX:55172800-55185600	Weak transcription	Primary T cells from cord blood	blood
24	chrX:55172800-55186000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chrX:55172800-55186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chrX:55172800-55186000	Weak transcription	Liver	Liver
27	chrX:55172800-55186000	Weak transcription	Brain Anterior Caudate	brain
28	chrX:55172800-55186000	Weak transcription	Dnd41	blood
29	chrX:55172800-55186000	Weak transcription	Hela-S3	cervix
30	chrX:55172800-55186200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chrX:55172800-55186200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chrX:55172800-55186600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chrX:55172800-55186600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chrX:55172800-55186600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chrX:55172800-55186600	Weak transcription	Brain Angular Gyrus	brain
36	chrX:55172800-55186600	Weak transcription	Brain Hippocampus Middle	brain
37	chrX:55172800-55186600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chrX:55172800-55186600	Weak transcription	Duodenum Mucosa	Duodenum
39	chrX:55172800-55186600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chrX:55172800-55186600	Weak transcription	Psoas Muscle	Psoas
41	chrX:55172800-55186600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chrX:55172800-55186600	Weak transcription	HMEC	breast
43	chrX:55172800-55186600	Weak transcription	NH-A	brain
44	chrX:55172800-55186600	Weak transcription	NHEK	skin
45	chrX:55172800-55186800	Weak transcription	Brain Cingulate Gyrus	brain
46	chrX:55172800-55186800	Weak transcription	Right Ventricle	heart
47	chrX:55172800-55187000	Weak transcription	Left Ventricle	heart
48	chrX:55172800-55187000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chrX:55175000-55177800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chrX:55175200-55175800	Enhancers	Fetal Heart	heart

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